The Ukraine military and, of course the Russian military, have BUK systems. It's unknown whether the Ukranian rebels have control of any of these systems (or something similar) or not, however, to the extent that the pro-Russian Ukranian rebels are supplied or augmented by Russia and possibly even by Russian Spetznaz commandos pretending to be Urkanians, the probability increases.
Flares would not work as a deterrent in this case. Long range SAMs are radar guided. Flares are intended to provide protection from IR-seekers, i.e. typical shoulder-fired, short range MANPADs like the US