No, it shouldn't matter -- just make sure to remove any language-specific package before upgrading, this way you can test that you don't get all of them installed all trying to obsolete the same package :-) (i.e. same scenario as you highlighted above)
Thanks for the comment gijom.
Since IMO not being able to scroll at all is worse that a non-functional minimap (and the work-around is identical to before) I will probably push the update anyway. I should imagine that minimap fix will probably come from PyDev project when they start building against newer Eclipse Platforms.