Don't worry your head about it... the structural design team will be re-working a lot of the older steel supports to the much lighter, yet stronger ANCR and borazon composites. As long as we don't bump into anything denser than we are, we shouldn't have to worry too much about it. It'd help if we had a lot more carbon to play with. We might need to retro-fit some of it in flight if we come across any carbonaceous chondrite bodies between here and Mars.
I'd still be a lot happier if we could generate artificial gravity and come up with a structural integrity field.
Long term, the only convenient source for carbon will be atmospheric scooping of the planet Venus. That's out of our way for this trip, although it is possible to do flybys upon occasion when one wants to cut time from a Hohmann orbit.
If we get a build-up, or outgassing of CO2 as was experienced by that ludicrous Biosphere, we can tap into that for additional structural development.
"... if we could generate artificial gravity and come up with a structural integrity field."
I can't do anything about the artificial gravity just yet, but we could play with artificial molecules for the structural integrity field. These are similar to what would be used in simulation, or "holodeck" chambers, and are unintelligent nanoscale devices that can be arranged in patterns.
Shouldn't we be able to 'flip' the telegib to 'teleroast' and convert raw material into carbon?
Since it converts solid matter into a subatomic plasma explosive, it shouldn't be too hard to have it convert stuff into into other forms of normal solid matter?
But then it would have been a viable teleporter to begin with instead of a strange weapon?
Hmm, ponderment.