You're not supposed to feel comfortable. You're supposed to be appalled at Blast Off's actions. This isn't sweet, it's horrifying. That's the entire point of the story.
My point is that you can be very disturbed at this story for the very legitimate reason that it is about a super disturbing topic. That makes it really easy to be disturbed by all the things in the story (like Onslaught's and Blast-Off's relationship). I still stand by my earlier thoughts. Just because something would be an awesome story doesn't mean you write that story.
It is disturbing. That's why I'm really disappointed it's ending so soon, and hope we see some resolution to it before it ends. I want to see if Blast Off can continue this charade or if his guilt causes him to admit to Onslaught what's going on. I would point out that Blast Off never had much of a good choice- he could choose this horrible path, but give the Combaticons (including Onslaught) back lives where they are citizens again with some status and resources and could likely save Onslaught from his own self-destruction (though yes, that shouldn't be Blast Off's choice to make, but Onslaught's).... or leave them all rotting on a slab where they either never wake up again or if they somehow do, they are prisoners or, at best, escapees on the run until they are hunted down and killed. Blast Off's loneliness at being left to rot forever inside a living shell, never able to contact anyone ever again, and facing the same fate for his teammates too, was also a horrible choice to make. There just were no good choices for him, thanks to Starscream and Airarachnid's manipulation.