RNAi is a single stranded RNA molecule that is complementary to and binds an mRNA molecule. This sets in motion a sequence of events that destroys the entire dsRNA: dicer first chops up the dsRNA into little fragments, then the fragments are broken down in the RNA induced silencing complex (RISC).
So, you're talking about LINEs and SINEs (long/short interspersed nuclear elements). LINEs are basically a copy and past mechanism in that they encode a ribosome; SINEs are cut and paste and do not make a copy of themselves. So, if you could sequence these elements and produce a complementary copy, I don't see why you couldn't use RNAi to stop their jumping around. However, why would you want to? They generally don't cause any problems. In fact, they're useful in terms of defining evolutionary relatedness and constructing phylogenetic trees.
I don't know what genomic imbalance is. . .apologies.