I've often thought of Sami Zayn as the Daniel Bryan of NXT in that they were both cast in the role of underdogs, both have a highly physical style of working, both had a strong indie following before signing to WWE and fans have rallied around them.
As a tag team, I think Bryan & Zayn would have no trouble getting over; Bryan's popularity is undiminished, pairing Zayn with him would very well only help Zayn and it could introduce a new dynamic into the tag team picture. Would they work well in the long run? I doubt it because in the grand scheme of things, if both are able to compete long term inside the ring, it wouldn't be too long before fans were clamoring for one or both of them to be moved to the upper mid-card/main event picture. It's something of a problem regarding tag teams in which one or both members is someone that a lot of fans believe can be/should be wrestling in the main event. As the OP pointed out, there have to be doubts among WWE officials, and justifiably so, unfortunately, as to whether they can continue as in-ring wrestlers; as a result, putting them in a situation where they can be protected to some degree makes perfect sense so that officials and the wrestlers themselves can get some idea how things are going to work out. Daniel Bryan's been in two high profile spots in which he's had to be pulled out of due to injury, so while I agree with the notion that he's better than this, or rather he would be better than this if he was genuinely healthy and could go in the long run, the doubt WWE officials have is understandable.
In Bryan's case, he's so passionate about wrestling that I honestly wouldn't be surprised if he asked to be released if WWE informs him that they don't intend to clear him to compete in the ring again. He'd have no trouble whatsoever finding work; he could easily go back to ROH or a bigger stage like New Japan. Unless Bryan sees that it's going to be too dangerous to proceed, which means he'll have to wrestle some in order to find out, then WWE is probably a safer environment in which to find that out.