Why would Burke need to smuggle a dangerous organism through ICC quarantine if the Company effectively owns the ICC? It's like how the new Colonial Marines book says the Company funds the marines; yet the mission to LV-426 was under military jurisdiction and a corporal could nuke a colony over protestations of a Company rep.
One way to rectify it is that Ripley's knowledge of the ICC and its quarantine was almost six decades out of date.
Another thing is that just because WY and ICC are cozy on everything - stuff like dangerous organisms from the colonies might one of the clear lines of demarcation or disagreement.
So... 90% of the time, WY gets what they want - but that other 10% gets "interesting"
Plus, Burke wanted to keep info as controlled as possible and even said so
"If I made a big deal out of it - everyone steps in and there's no exclusives for anyone."
So, smuggling it in past ICC minimizes the amount of "shares" and "graft" involved...
For LV-426: "The company co-financed that colony with Colonial Administration" ~ Burke on Gateway
So, Acheron was more of a Joint Venture which always comes with a ton of weird politics and loopholes and such.
And, those protestations were after same said marines were told they were candidates for space jettison in the quest for some skeezy corporate exclusive... that also happened to traumatically kick their assets to the curb just hours before.
17 weeks in hyperspace at military speed still means a court martial is months away - if ever.
I can see the "local command authority reacted to a clear and present danger" in the after action report even if there was a court martial.
And finally - if ICC had evidence (like a marine debrief) of stuff WY was doing under cover of darkness... well that might alter the equation too.
Burke seems to have had enough snap to keep plausible deniability in mind to "save the company reputation impact"
So, lots of ways to play it...
We live, as we dream -- alone. ~ Joseph Conrad