It's true that in the show, Michael does explicitly call Toby out for being part of "corporate". There are a couple reasons why I don't think that meant he should have been removed when Sabre took over (though the two reasons are tied together).
For one, Michael himself claims that he is part of Corporate. Since it's Michael that brings it up both times, it seems like if Sabre fired Toby, they also would have fired Michael. This happens in S02E02 - "Sexual Harassment". Michael Scott says:
"I am so used to being the bad boy. I am so used to fighting corporate, that I forget that I am corporate; upper management."
Video of scene from The Office Youtube channel, timestamped 2:39
The other reason ties in why Michael, Toby and Holly all kept their jobs. It was as David Wallace said when he told Michael about the buyout; they bought Dunder Mifflin specifically for the sales offices. Those were what worked.
As far as I remember, not a single office worker was fired when they merged with Sabre. Sabre just added their own oversight and communication by having Gabe around, and many things about the office remained essentially untouched. After all, if it ain't broke, don't fix it.