I think it's been posted that there's a way to tell the App Store to disregard unwanted updates, but I can't verify it.
There is, according to Urquhart*, but it requires access via App Store which I can't access in finite time (if at all) and even so there are restrictions on what can and cannot be disregarded.
[* ... you can selectively disable (hide) existing notifications about specific software updates you don't care about by control-clicking the update inside the App Store to reveal a hidden "Hide Update" option. It is not available for everything, though (some apps).]
