Some people are repulsed at the mere sight of javascript in the web. Personally I think such position is not really justified. Yes, it is true that the current web is a broken mess, and javascript is to blame for that to some extent, but like everything, its the use we give it that matters.
Personally, I think that if its use is justified, the script is "homemade" (meaning that it is made by the same person(s) who made the website), and it's hosted in the same place as the page, its just fine.
At the end of the day its just a scripting language that runs in the client (browser), some things wouldn't be possible with something like that.