No, here's why:
The way to lose your apps is by restoring the phone and setting up as a new phone, or going into the apps tab and I checking the sync box.
What you want to do is stay in the main iPhone/ipod touch tab (To get to the iphone tab find the devices drop down in the list of iTunes libraries, playlists, links, etc on the far left of the iTunes window. Then choose the farthes left tab, where you normally go to check for iPhone/ipod touch updates.)
Scroll down you'll find a cluster kind of like a check list. In there somewhere is "manually manage songs/videos" check that box.
That's where you want to start. Once youre there refer to my earlier post.
(At the risk of repeating myself: Once you're manually managing you can go straigh to your idevice and swipe the songs you want to delete to delete them. Then delete them from your library. Then go uncheck the "manually manage" box and sync again.)