I've read some discussion about removing jQuery from Construct and from what I understand that is not likely to happen in the near future but from a different angle; will the jQuery version that is included (1.6.3, release Sept 2011) be updated in lue of removing it (the current release is 1.9.
Since the 1.6 release there have been many fixes especially dealing with some of the newer browsers.
Note: I replaced the 1.6.3 version with 1.9.0 and while I am not yet using Construct on large heavy projects I have seen no issues when testing with the examples and such.
Ken