Space Marines are very powerful but won't necessarily break the game, especially if he's only dropping in occassionally. In my game we have an arch-militant specialised in basic weapons carrying a boltgun. Until I changed the righteous fury rules over to d5 on the appropriate crit table he was fully capable of one-shotting fairly major enemies on a regular basis. Plus our RT is a fast-talking con-man trade machine so the arch-militant has best-quality muscle implants and a suit of light power armour. Our games still work.
Some ideas for using your (slightly) beefier astartes PC:
1. You're playing Rogue Trader and he's a marine. There will be a lot of social interaction and business deals going on that he has no interest or capacity for. "Brother X, we're heading out to a local bazaar to ask around and set up some business ventures. You want to come?" "No, I must strip and clean my holy boltgun while reciting prayers to its warrior spirit."
2. Depending what kind of renegade he is (Just got seperated from his chapter? On a special one-man mission? Disagrees on certain Imperial practices?) he will hold a very narrow view as to what is acceptable. Your crew finds an interesting and highly profitable planet/relic/xenos breed: if it isn't fully bathed in the glorious light of the Emporer it's going to need to be purged.
3. These fluff considerations could just be flavour for the character though, there are ways to get him to play nicely with the other children. Renegade does suggest he might be a bit more liberal in his beliefs than standard astartes indoctination allows. It might be the whole reason he's off on his own and needing to pick up jobs with a Rogue Trader instead of raining death on the enemies of mankind with his brothers.
4. He might need to adapt and accept some of the crews' more morally grey endeavours. Bolter ammo doesn't grow on trees and repairing astartes-scale power armour is a very specialised and expensive process. Plus there aren't that many opportunities to hitch a ride from planet to planet, especially if you're a rogue marine. He may just have to adjust his usual standards to work with the only people who can provide what he needs.
These ideas can lead to an interesting dynamic where the crew and the marine don't see eye to eye on a lot of issues but each party offers something useful to the other. And if you go with the special mission/one man strike force hook there are all kinds of potential stories from there. And that can explain what the marine is off doing when he's not with the crew. Or maybe he's pursuing his own agenda alongside their goals and has to recon or possibly get revenge on something they're searching for or working with.
I don't know if you had any plans for a specific chapter, but a Space Wolf would work well. Or go completely the opposite direction and he's an Alpha Legion operative who just shows up to 'help' the crew as part of a large scale scheme that could potentially come back and bite them in the long run.