I think Janeway felt it was somewhat out of character which is why she had qualms about some aspects of it, possibly it's the first time she'd included sex with her regular use of the holodeck. She'd bonded with holograms before but it had been the same way you might bond with an MMO character of your creation or an NPC in a game who you really like interacting with. Leonardo etc.. adding the sex shifted it to another level for her and that's what threw her.
I don't think she was going to "great lengths" doing it though. I think she saw it as a normal, something to encourage unpartnered crew members to engage in given their circumstances in the DQ. Eventually when everyone else is doing something your personal squeamishness about it breaks down, why not give it a whirl? It's not like giving Chak a whirl where you have to look at him every day afterwards for seventy years, you just walk away and end program.
So she tried it. And she couldn't quite handle it. And in the end she was okay about that.
