I think the real reason Aziraphale agreed to go back to Heaven was because the Metatron hinted that he knew about their body swap, that Aziraphale wasn't actually immune to Hellfire, and Crowley wasn't immune to holy water.
As Crowley himself pointed out, they had become much less careful about hiding their relationship over the years since Season 1. Crowley openly clings to Aziraphale in front of Muriel.
Aziraphale doesn't deny being an item with Crowley in front of Shax, and so on.
That's because the fact that Heaven and Hell now know about their connection, whatever they think it is, no longer scares them. Heaven and Hell believe the two of them are impossible to destroy, and Crowley and Aziraphale know that, so they don't bother hiding nearly as much anymore.
So I don't think Aziraphale was frightened by the fact that the Metatron knew about their friendship. I think what truly scared him was the possibility that the Metatron had figured out their body-swap scheme.
Metatron says that he has “been looking back over a number of his previous exploits”(Notice how he pauses before "previous exploits"), mentions that he knows about the fact that in some of them he formed a “partnership with Crowley,” and then immediately says that Aziraphale can appoint him as an angel. From Aziraphale's perspective, the thought process could have been:
"What exactly did he find? Could he know about the body swap?"
And perhaps the offer to restore Crowley as an angel was itself a subtle hint: "He already took on your angelic form once, why not make him an angel for real?"
I don't know if I've explained this very well, but I hope you understand what I'm trying to say.
