Hmmm. This ties back into the problem with prequels. If Discovery (and the Federation by extension) helped the Romulans, then why would the Romulans want to attack Federation Outposts in the Neutral Zone 10 years later?
Romulans don't believe in loyalty. They do believe in maintaining the balance of power however. Seems totally logical to me to try and save the Federation to hold back the Klingons, only to turn their backs on the Federation again.
Also, you could have the Romulans try and steal the spore drive technology. Ash Tyler as some sort of Romulan sleeper agent (even if rescued from the Klingons) would be a bit more believable, due to the need for less cosmetic surgery (though they'd have to do a total blood transfusion or something). Maybe he originally had some mission within the Federation, was captured by the Klingons, and incidentally ends up on Discovery. Then when Discovery meets the Romulans they pull him aside and awaken him with new orders.
Where this would make the most sense to have it would be around when "Lethe" takes place, when Cornwell is thinking about taking Discovery away from Lorca. Starfleet Command would be wondering "What the Hell is going on with this Captain?"
I was thinking more along the lines of the ship happening to have a mission there when the attack started, which results in a protracted battle where it's not safe to beam up from the surface. Or maybe the Klingons drop something like an EMP which knocks out all ground-side communications. I would say Lorca, Michael, and Tilly should be on the surface (Tilly could be the Nog of the episode, experiencing the trauma of war - though hopefully not losing a leg), while Saru and Stamets stay up in orbit.
I agree that it would be a good idea for Discovery meeting with a rebel/dissenting faction of the Klingon Empire. In the actual series, L'Rell is effectively the dissent since she was secretly against Kol.
But where we run into a problem is with there being an alliance with Augment Virus Klingons. Why? Because Augment Virus Klingons are who the Federation is at war with in TOS.
My take was that the Federation established peace with the Klingons thanks to L'Rell, a lot of Klingons weren't too happy about that, and once something happened to L'Rell and she was out of the picture -- plenty of time for that to happen between DSC S2 and TOS S1 -- then hostilities would resume, even if not outright hot war.
The Klingon empire is shown as being quite different by TOS - less feudal and set up more like an authoritarian state. If I were to hazard a guess L'Rell was couped by her second-in-command, who just co-opted her existing centralized power structure.
But if I were rewriting from the beginning, L'Rell as we saw her wouldn't exist. The first season was way to economical with named Klingons, having only four matter across the whole season, with L'Rell making a reverse heel turn because she's the last named Klingon standing. Mary Chieffo does good work though, so I'd still want her in an analogous role.
I really did like the Mirror Universe twist/arc in Season 1, but I felt it robbed a satisfactory finish for the Klingon War, which led them to just tack on an ending. I much rather would've liked the Mirror Universe twist to be the season finale, after they had finished the war arc. And Season 2 could've been about the Mirror Universe, perhaps all set in there.
My hope at the end of Act 1 of the first season was that Discovery would become something of a Flying Dutchman/Sliders on a starship - a ship lost because it cannot quite find its way back to the original timeline. The show then becomes about exploring the multiverse as a whole.
Obviously, they had different ideas, and dialed the Spore Drive way back.
But I do think the MU would have been better left to Season 2.