This should do the trick:
(add-hook 'web-mode-hook #'(lambda ()
(unless (and (stringp buffer-file-name)
(string-match "\\.js\\'" buffer-file-name))
(aggressive-indent-mode))))
It activates aggressive-indent-mode only if file extension is not js.
If you use (global-aggressive-indent-mode 1) you can disable it per this:
(add-hook 'web-mode-hook #'(lambda ()
(when (and (stringp buffer-file-name)
(string-match "\\.js\\'" buffer-file-name))
(aggressive-indent-mode 0))))
And finally, to disable it in javascript sections use these advices:
(defun aggressive-indent-advice (org-fun &rest args)
"Do not agressive-indent in javascript section of web-mode."
(let ((agressive-indent t))
(when (equal major-mode 'web-mode)
(setq agressive-indent
(not (member (get-text-property (point) 'part-side) '(javascript)))))
(when agressive-indent
(apply org-fun args))))
(advice-add 'aggressive-indent--keep-track-of-changes :around #'aggressive-indent-advice)
(advice-add 'aggressive-indent--indent-if-changed :around #'aggressive-indent-advice)
(advice-add 'aggressive-indent--softly-indent-defun :around #'aggressive-indent-advice)
Note that, depending on your need, you can use the former two hooks independently from web-mode to disable aggressive-indent. On the other hand, the depends on web-mode, but will also work for .js files in web-mode.
