Two problems:

• org-indent-mode is a minor mode and like all minor modes is enabled by calling with a positive argument and disabled by calling it with a negative argument - see its doc string with C-h f org-indent-mode. So you have to call it like this: (org-indent-mode -1) to disable it.

• org-to-tree-indirect-buffer leaves the current buffer unchanged, i.e. that of the original Org mode file. However, you need to turn off org-indent-mode not in the original buffer but in the generated indirect buffer. Fortunately, it saves that indirect buffer in the global variable org-last-indirect-buffer, so you can use with-current-buffer to temporarily switch to the indirect buffer and disable org-indent-mode there.

The final form of the function would then look like this (EDIT: the fontification of the buffer was lost when executing the original form of the following function, so I added an explicit call to font-lock-fontify-buffer to restore it, although this is probably a workaround, not the real solution. However, I still cannot reproduce the OP's problem where he loses org-indent-mode in the original buffer) /EDIT):

(defun my-org-to-indirect-buffer ()
  "Run `some-command' and `some-other-command' in sequence."
  (interactive)
  (org-tree-to-indirect-buffer)
  (with-current-buffer org-last-indirect-buffer (org-indent-mode -1))
  ;; the original buffer loses fontification for some reason, so we restore it explicitly
  (font-lock-fontify-buffer))

One more problem might be the key binding: why do you bind it in the global map? Presumably you only need it in an Org mode buffer, so why not restrict it to the mode-specific keymap? Something like this:

(define-key org-mode-map (kbd "C-c f") #'my-org-to-indirect-buffer)

Two problems:

• org-indent-mode is a minor mode and like all minor modes is enabled by calling with a positive argument and disabled by calling it with a negative argument - see its doc string with C-h f org-indent-mode. So you have to call it like this: (org-indent-mode -1) to disable it.

• org-to-tree-indirect-buffer leaves the current buffer unchanged, i.e. that of the original Org mode file. However, you need to turn off org-indent-mode not in the original buffer but in the generated indirect buffer. Fortunately, it saves that indirect buffer in the global variable org-last-indirect-buffer, so you can use with-current-buffer to temporarily switch to the indirect buffer and disable org-indent-mode there.

The final form of the function would then look like this (EDIT: the fontification of the buffer was lost when executing the original form of the following function, so I added an explicit call to font-lock-fontify-buffer to restore it, although this is probably a workaround, not the real solution. However, I still cannot reproduce the OP's problem where he loses org-indent-mode in the original buffer) /EDIT):

(defun my-org-to-indirect-buffer ()
  "Run `some-command' and `some-other-command' in sequence."
  (interactive)
  (org-tree-to-indirect-buffer)
  ;; turn off org-indent-mode in the indirect buffer
  (with-current-buffer org-last-indirect-buffer (org-indent-mode -1))
  ;; the original buffer loses fontification for some reason, so we restore it explicitly
  (font-lock-fontify-buffer))

One more problem might be the key binding: why do you bind it in the global map? Presumably you only need it in an Org mode buffer, so why not restrict it to the mode-specific keymap? Something like this:

(define-key org-mode-map (kbd "C-c f") #'my-org-to-indirect-buffer)

Two problems:

• org-indent-mode is a minor mode and like all minor modes is enabled by calling with a positive argument and disabled by calling it with a negative argument - see its doc string with C-h f org-indent-mode. So you have to call it like this: (org-indent-mode -1) to disable it.

• org-to-tree-indirect-buffer leaves the current buffer unchanged, i.e. that of the original Org mode file. However, you need to turn off org-indent-mode not in the original buffer but in the generated indirect buffer. Fortunately, it saves that indirect buffer in the global variable org-last-indirect-buffer, so you can use with-current-buffer to temporarily switch to the indirect buffer and disable org-indent-mode there.

The final form of the function would then look like this:

(defun my-org-to-indirect-buffer ()
  "Run `some-command' and `some-other-command' in sequence."
  (interactive)
  (org-tree-to-indirect-buffer)
  (with-current-buffer org-last-indirect-buffer (org-indent-mode -1))
  )

One more problem might be the key binding: why do you bind it in the global map? Presumably you only need it in an Org mode buffer, so why not restrict it to the mode-specific keymap? Something like this:

(define-key org-mode-map (kbd "C-c f") #'my-org-to-indirect-buffer)

Two problems:

• org-indent-mode is a minor mode and like all minor modes is enabled by calling with a positive argument and disabled by calling it with a negative argument - see its doc string with C-h f org-indent-mode. So you have to call it like this: (org-indent-mode -1) to disable it.

• org-to-tree-indirect-buffer leaves the current buffer unchanged, i.e. that of the original Org mode file. However, you need to turn off org-indent-mode not in the original buffer but in the generated indirect buffer. Fortunately, it saves that indirect buffer in the global variable org-last-indirect-buffer, so you can use with-current-buffer to temporarily switch to the indirect buffer and disable org-indent-mode there.

The final form of the function would then look like this (EDIT: the fontification of the buffer was lost when executing the original form of the following function, so I added an explicit call to font-lock-fontify-buffer to restore it, although this is probably a workaround, not the real solution. However, I still cannot reproduce the OP's problem where he loses org-indent-mode in the original buffer) /EDIT):

(defun my-org-to-indirect-buffer ()
  "Run `some-command' and `some-other-command' in sequence."
  (interactive)
  (org-tree-to-indirect-buffer)
  (with-current-buffer org-last-indirect-buffer (org-indent-mode -1))
  ;; the original buffer loses fontification for some reason, so we restore it explicitly
  (font-lock-fontify-buffer))

One more problem might be the key binding: why do you bind it in the global map? Presumably you only need it in an Org mode buffer, so why not restrict it to the mode-specific keymap? Something like this:

(define-key org-mode-map (kbd "C-c f") #'my-org-to-indirect-buffer)