If she's a Rogue Trader, a big part of being the captain is going down to a planet's surface and kicking righteous ass in the name of Profit. It'd be good to know what direction you're going as you do it.
As to your question, OP, there are sooo many ways this could end in tragedy. My big worry if I were trying to do it would be the fact that the first spore that grows up into a Mek is going to result in half your ship's components being torn out and turned into "roight proppa Orky tek" before you can blink.
Then there's the problem of keeping the Boyz and Grotz and Squigs AND spores all contained. It's all very well and good to say "seal off a section of the ship and let them grow in there," but to do it properly and safely you're going to have to truly make it a completely isolated habitat. That means a separate power source and air filtration system. And every single room in your Ork habitat has to be strong enough to withstand the damage that comes from the Boyz scrapping with each other, Meks and Grotz trying to tear the place apart to make stuff, fires from the inevitable fungus-beer-Molotov-cocktails some bored Boy puts together, and the occasional squig trying to gnaw its way through the deck because it's hungry and the floor looks like the biggest meal in the place.
And THEN, once you get all that done, you get to figure out how to get them to use the boarding craft properly (like hell they're gonna let some humie drive them around) and how to tell one ship from another AND how to properly dock with another ship (you may just be better off shooting them into the other ship with drop pods, so enjoy that extra expense).
With all that taken care of, if you can get the non-Ork crew to be okay with it and keep any Inquisitorial or Ecchlesiarchal ears from hearing about it, you should be okay.
Until the Squiggoths start growing.