Assuming it's your CB500 that you're talking about, no, chopping off the tabs will not affect structural integrity.
FWIW, though, when shaving my frame (passenger pegs, horn mount, sidecover mounts, etc.) I gave serious thought to removing the centerstand brackets, and decided not to just yet, primarily because the centerstand was so useful at the time. (I was doing a lot of work on it.)
A couple of years later, I'm very glad I didn't, as I am ordering race pipes for the bike and they will prevent the use of the sidestand, ie. the centerstand will be the only option short of leaning the bike against a tree or something. In that light -- and considering that the centerstand brackets are essentially invisible -- I'll add my voice to those who suggest you not worry about 'em.