Yes, DTI policy is to discourage time travel whenever possible. And in Lucsly's view (and, frankly, mine), Admiral Janeway's action, using time travel and disrupting the entire continuum merely to make life relatively better for her own crew, was an incredibly selfish and frivolous abuse of time travel, and moreover, one that she initiated. She wasn't trying to correct damage caused by someone else's time travel, she was the one who chose to create a disruption to the flow of history. And Captain Janeway, by voluntarily going along with that illegal act even though she was fully cognizant of its illegality and immorality, was just as guilty as her future self.
But if you'll recall, when Lucsly and Dulmur were talking to AD Kreinns about their possible responses to Janeway's crime, they did broach the possibility of using time travel themselves to undo Janeway's alteration to history. And that shows that the DTI does not completely rule out the possibility of using time travel to counteract time travel and restore the "proper" history. It's an extreme measure and an absolute last resort, and only the administrators and senior agents are cleared to even contemplate it, but the option exists.
What happened to Shelan was also a temporal violation, an alteration of the proper history. More, it was an attack on the department itself. Think of how the police respond to a cop-killer. One of their own was victimized, so they were willing to do whatever it took to save her. Really, the "contradiction" was the whole point -- the fact that they were willing to contemplate using time travel themselves was meant to underline just how intensely they felt about this. If you've seen Doctor Who
: "The End of Time," think about the scene with Wilfrid offering the Doctor a gun. When a character is suddenly willing to do something he'd normally never contemplate, that's when you know a line has been crossed. (TV Tropes calls this the Godzilla Threshold
Although ultimately they decided not to take such action, to honor Shelan by being true to the principles she gave her life (literally her entire