The end of Tsyklon launches from Plesetsk (and it is unlikely that there will be launches from Baykonur either) will not affect the military space program - the last time the launcher was used to launch a military satellite was in December 2001. It was a launch of Strela-3 satellites, which since then have been launched by Kosmos-3M launchers.
Kosmos-3M, of course, is a "dirty" launcher itself, which the Space Forces hopes to phase out in about five years. Let's hope that the Angara rocket will be ready by then.
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It looks like Tsyklon might be used for launches from Baykonur after all.
Roscosmos reports that it would consider upgrading Tysklon-2 launch complex there to Tsyklon-4. But it is still unlikely that the launcher will be used for military launches - the rocket is manufactured in Ukraine.