The entry holes are clean enough to measure; there is no ruler in the photos, but I presume the reports are not lying. If that is so, where would rebels get a 30mm airplane gun, and how would they position it and the debris to get the required angle of entry? I'm pretty sure that you cannot hold that gun in one hand; and you can't even hang it from a crane, as it is bound to have some serious recoil.
The GSh-30-2 is carried by the Sukhoi Su-25 ground attack plane and in external gun pods. It measures 2044 × 222 × 195 mm, with a barrel length of 1500 mm and a weight of 105 kg.
But the final proof can be obtained only if the investigators can trace the same bullet, or the same pattern of bullets, through both sides of the cockpit. That would be possible only if the bullets (or the shrapnel of the missile's warhead) was shot at an intact airplane.