You know, when the Klingons find out Sam has one of their weapons, they're gonna be majorly pissed off!
As far as the Matrix goes, I think it is safely ensconced in Prime's chest. You notice that none of the others volunteered to take Prime's place when he told them of his plan. I don't think fear was an issue 'cause Ironhide doesn't have any and he should have stepped up to the plate first to offer to do it instead of Prime. I think it was because the others knew that they COULDN'T do what Prime was proposing. The Matrix, in tandem with Primes own spark was likely the only thing that could have done it short of Sams solution of a full-on discharge of the thing. Personally, I think if Prime had merged the All-Spark with the Matrix and his own spark we would all have been witness to the second coming of Primus...but that's just my opinion.