Removing rpm files won't hurt anything other that your ability to easily re-install said rpms without the bother of downloading again. Once the rpms are installed, the rpm packages are extra baggage. Not used in an running system.
I suspect that the upgraded kernel isn't configured correctly for your hardware. So, you could try booting from a live cd, mounting the partitions of the affected OS, and chrooting into that OS to see if you can do a kernel reconfig and compile.