If you correctly ./configure
the program then make install
should overwrite the already installed binaries. I relied on this when installing Fluxbox. The 0.1.14 rpm set up the menu entry in my gui login screen, and then with ./configure --prefix=/usr
(Mandrake and Redhat differ to other distros there) I overwrote the fluxbox binary with the latest releases.
Your rpm database will still think the original rpm file is installed, and I dunno if it runs file checks before running the uninstall script.