There is a difference between someone who rationalizes and someone who is rational. Seka was rationalizing her poor choices. Her entire argument and lots of these points are moot... Seska made her choices, wound up dead, and Voyager got home...
Seska doesn't have the benefit of 20/20 hindsight that we do. She felt that Voyager needed protection. This is rational, as we know they did. The Kazon were willing to offer that protection, and Seska was willing to make a deal with them. Janeway was not willing, nor even Chakotay, so Seska had to carry this out this in secret. By chance, the Kazon made a mistake in using the technology Seska gave to them, and by an even greater chance, Voyager found out about it. Seska could have come clean, but we know this isn't in her character(from episodes like Prime Factors), so she had to cover her tracks, and she had a contingency plan. It stands to reason that she had an ally(Jonas) on Voyager that helped her help the Kazon, and perhaps this is what she had on him in the second season.
And like I said, if she had not fled Voyager, she would have lost all control of the situation and been at the mercy of Janeway, who might have deemed her too dangerous for even the brig and put her off the ship(just like Kirk did to Khan)
BTW, The Borg knew of the Kazon. So they must have had a presence in the area.
The Borg knew of the Federation, the Ferengi, the Romulans, and the Klingons, yet had no presence in their regions either. The Borg can go wherever they want. The Borg knew of the Talaxians also. Seven says they assimilated a Talaxian transport. The point is, from Seska's perspective, there are no Borg. Voyager doesn't even get wind of them until they are far out of the region where Kazon can be found. It's not a factor in her decision making process.
How did she become so evil though?
At first she was driven by understandable motives and yes, she was a Cardassian spy, but by the time of that hologram episode, she was sadistic.
It was like she went from being anxious to get home, to being desperate, to being totally evil.
Well, not including the holodeck episode, she wasn't exactly evil, but she wanted Voyager, and promised to help Cullah seize it as part of her arrangement with him. The Voyager crew had become her adversaries, so from the perspective of the heroes(and ours), she is now their enemy.
As for the holodeck episode(which imo, is a really, really great episode, and great to see Seska as a Bajoran again), perhaps it's showing her true colors and vindictive spirit. Tuvok was creating this program in secret. No one else knew about it, so the plan probably was that Tuvok would go into the holodeck(alone) to work on his training program, and later be found there dead, and the crew would be none the wiser as to the cause. They would say "Tuvok was working on a holoprogram and somehow the safeties were deactivated and a terrible accident happened"
She really hated Janeway, and killing Tuvok(with "poetic Justice" from her perspective) would demoralize her to a great degree.
We see in DS9 that Garak, even though he could be the most pleasant person to talk to, and a great ally, also had this vindictive spirit, and was capable of great evil. We learn that he took pride in his torture sessions, and never had to be asked to do any dirty work, as he delighted in it, and was highly motivated