Yep, you'd just have to delete a couple of files from the romfs folder in Wilting Y first; a/0/8/2 (this contains the story text) and possibly a/0/7/4 (this is game text, so things like descriptions for the new TMs and moves with different effects. Might be best to leave it at first and delete it later if needed).
And just to clarify, those names are file paths, so a/0/8/2 is a file named "2" in a folder named "8", in another folder named "0", etc. Other than that there shouldn't be any problems with patching Wilting Y over Neo Y.