The Russian military seem to be preparing to end military activity at Baykonur in two years. According to an article in a weekly that covers military industry, VPK, the commander of the Space Forces told reporters that the miltiary have already made the decision to withdraw from Baykonur. The Space Forces facilities at Baykonur will be handed over to Roskosmos.
As far as I can tell, the withdrawal will not affect launches of military satellites - Roskosmos will continue to handle them when necessary. But the test launches of ICBMs will be discontinued - Popovkin mentioned that all of them will be completed by the end of 2007 (at the rate of one or two launches a year). But launches of SS-18 have already been moved to Dombarovsky. The missile that is going to be affected the most by the withdrawal is UR-100NUTTH/SS-19 (which Russia is going to keep in service). Would the remaining three to four launches (and launches of Rockot) provide enough data to keep SS-19 operational? Quite possible. But it is also possible that the Rocket Forces have some other plans for SS-19 test launches.