The problem is Subnucleonic Beam, not Viral Matrix. Although I think Viral Matrix should still let you fly and turn, there is at least an easily available counter. To Subnucleonic Beam, there isn't. Get hit with it and do nothing for 20 seconds, i.e. just die.
As a RA5 sci captain, i think snb should be reworked that you could use at least shield facing power rerouting, in order not to die too quick, or maybe affect just weapons. Currently at full aux my snb hits for approx 30s, and if the guy is not in a carrier, and havent hit any STRONG defensive skill before being hit, its usually a death sentence, like vm was before the fix of ST (APO alway worked against VM)