If intangibility works (and I personally think it probably will, considering we have no proof Shaw can tank having a fist suddenly materialise in the space where his brain or heart used to be), then Reverse Flash absolutely stomps. At best this is a stalemate in anyways, as Shaw won't lay a finger on Thawne.
Ok, even if we say for argument's sake that Shaw could absorb some of the energy from the vibrations (which is debatable IMO), it still won't actually stop Thawne's hand from going into his head. Being amped won't mean much when you have a fist in your brain. And again, even if that doesn't work, which it should, Shaw will never ever tag RF.
Bullets have a finite amount of energy after being fired (a hell of a lot less than a speedster). The only way your plan would work is if Shaw literally managed to totally drain any power Thawne has in that split second he sticks his hand through his head, when we know that Thawne can vibrate himself for extended periods of time. Unless you are trying to claim that Shaw can actively suck the speed force from Thawne, in which case you have to prove he can, even though the speed force itself isn't directed at Shaw but at Thawne himself. The nuclear reactor didn't immediately shut down when Shaw started absorbing the energy it generated. It kept producing power which Shaw just kept sucking up. The energy is already generated, because of Thawne using his powers to vibrate himself, by the time Shaw absorbs it, so again, won't make a difference. Unless, like I said, you want to claim that Shaw can suck the speed force from Thawne, in which case you have to prove it.
If he could, he would have been able to freeze people in place in the movie with nothing but a finger touch. His powers are simply absorbing various forms of energy directed at him, once it comes into contact with his body. He can then use this energy in various ways, like either projecting it, or using it to amp up his strength. The kinetic energy is already generated by Thawne, using the speed force to vibrate his atoms, by the time Shaw absorbs it, so it getting sucked up won't affect him directly. However, RF would eventually grow tired from the exertion. So, for example, if Reverse Flash stood in one spot and vibrated, but didn't go intangible, and Shaw stood there holding him while he did it, Shaw would get a massive amp over time, and RF would eventually exhaust himself, at which point Shaw would probably be strong enough to punch his head out of the vicinity. But RF literally only needs to keep enough juice to perform one head phase, and it is game over.