Sleeping with subordinates—not allowed
Many of the romance options are with comrades, not subordinates. Your Shepard may have abused her position of authority, doesn't mean everyone did!

Characters like Liara, Tali and Garrus are all on board as comrades in arms either as private citizens or representatives of their own governments/military forces. Jack, during ME2, was a private citizen. Etc.
But getting to Kelly specifically, she was a Cerberus Operative, not Alliance military, so any repercussions would depend on Cerberus regulations, not military law. Any relationship with her would therefore not be subject to a court-martial, rather it might lead to her sacking from the organisation.
Or, more likely, a promotion based on forging a strong tie with Shepard, potentially keeping her on their side to do what the Illusive Man wanted her to do...
Desertion and aiding the enemy—not allowed
Shepard was KIA and, during her tenure working alongside Cerberus they were not an outlawed organisation. This is evidenced by certain Citadel security systems being provisioned by Cerberus in ME3.
The military had declared her dead, not deserted and Cerberus wasn't the enemy at the time. No case to answer.
Reckless disregard for civilian casualties—not allowed
Your Shepard, not everyone's Shepard.
Reckless disregard is not allowed but if the casualties can be justified, they're allowed. I don't know the circumstances surrounding condemning billions to die so I don't know if your Shepard would have been able to justify it in the context of the greater war.
My Shepard's in the clear on that one, too!