With "Vaulting Ambition" we have the intriguing possibility [spoilers!] that we could end the season with no more Lorca and no more spore drive. This would be pretty exciting from a series-concept point of view: each season could have major characters and MacGuffins that define the arc of that season, with each season being thematically distinct from each other.
It's not quite Star Trek: Sliders, but it's closer than anything we've had before!
Aside from any lingering trust issues I would imagine Saru still has with Burnham, surely he doesn't actually have the power to appoint her into a command position after she's been booted out of the fleet? But then this show doesn't seem to pay much heed to realistically depicting any kind of military organization/discipline (e.g. everybody constantly hiding obviously dangerous threats for emotional reasons; Lorca just ignoring everything the admirals tell him to do; etc.).
It would be more like this show to throw us a curveball and bring in someone totally unexpected. Captain Owosekun!!
Back to the main protagonist being the captain?
Oh. Oh my.
Of course saru could decide he is not up to it and let burnham take command.
Yes, these are all possibilities. From a meta perspective, I wonder if the producers were looking for a way to continue on without Jason Isaacs if there weren't enough of us subscribing to be able to afford him ... but also to be able to continue with him if there were. But I think Kev points to a real concern about losing Lorca: Saru would be in charge, and that doesn't seem likely to drive a lot of narrative conflict going into the next season. But I've been surprised at every turn so far!
Saru as captain of the Disco, permanently?
I think the spore drive will cease to be used at some point but probably after return to the prime universe. Lorca probably has no future in the prime universe so he may indeed end up gone.