Slip speedily in (faster than a fighter even), right under their noses.
Actually, if you make a class dedicated to this, I think a fighter engine is faster. You only need a single command module and fuel storage, which are light enough that I don't think the FAC engine's higher total power makes up for its higher mass. What's more, the fighter engine has a lower thermal signature.
That said, I don't think this will really work. Even as fast as it is, it'll probably take at least a few minutes to get through the aliens' sensor range, and a little ship like this won't be able to survive anything more threatening than a couple countermissiles. It's reasonably likely to work anyway if you use a big enough time increment, getting in and out in one sub-pulse, but that's a bug, really.