Matt you know that you can fit a company of marines and all their toys on a (much smaller) Strike Cruiser with room to spare. Chapters operated out of cruisers during the Heresy Era with no trouble at all.

Also, marines don't take up all that much space. Think about this: we can, right now, fit 5,680 people on a 332.8 meter long carrier (Nimitz Class) designed to hold a huge number of aircraft which, while nowhere near the size of a thunderhawk, still take up a considerable amount of space. While a marine ina rmour would most likely find the corridors in such a ship impossible to navigate, the scale should still make a point on its own. Even if you doubled the size of the rooms to account for it, you'd still get a good 2000 people on it.
Incidentally, Thunderhawks are barely pushing thirty meters. Source [url=http://wh40k.lexicanum.com/wiki/Thunderhawk#.U4vVDChqFNU] (Taken from a Forge World Imperial Armour Book, which is only one step removed from a Codex in terms of Canon.)

I'm pretty sure you could comfortably downsize to a 2km cruiser and keep all the toys, and if its a heresy era ship, as many are, it may very well have a teleporter. Also, the mechanicus can still build a lot of their lost tech, they just cant improve it as they don't understand it, as well as generally taking a very long time to build it.