I'd keep it simple and just nix the guns from the existing Assault Transport. Even as purely "Stealth/Utility Transports" I'd use the hell out of them, purely because it's a pain to herd a fleet under Cloakers, plus they are vulnerable to the cloaking hiccup on system entry issue (latency introduced when the game has to step through thousands of units on a heavily-populated planet, it can result in a gap between the ship appearing and the cloaking check picking it up, in case you are lucky enough to have never encountered this irritation -- absolute ragemaker when it happens on a planet with a Warhead Interceptor).
IMO, the main source of the problem with ATs is how much of a "greater than the sum of its parts" boost it produces when you stuff the flying lunchboxes full of weak, high-cap, cheap fleetships. They end up more than double-dipping as they either gain or lose no per-pound DPS by trading their attack in for the ATs, and the drastically boosted lifespan produces an immeasurable gain if you look at it from a "Damage Per Lifespan" perspective. There's not really any tradeoff, other than losing whatever special perk (teleportation, FF bypass, etc) that the unit may not even have had anyway.
I don't think it's much of an issue when filling them with starships, both due to their low numbers not being able to push the AT attack up to the max, and because they're already tanky and hit hard (at least certain types), so they don't get the synergistic extra life + no damage loss == effectively loads more damage over time.
An alternative to completely removing the attack from ATs, so they can keep something of an "assault" flavor, would be to replace the damaging attack with something more crowd-control related. Maybe a short-duration, short to moderate range AoE stun on unload -- that would combine nicely with doom-dropping the fleet in hostile territory both mechanically and thematically. If it ended up being abusable, stick a recharge on the drop-stun AoE. Similarly, if there's currently an issue with people pulling rapid unload/reload shenanigans, stick a delay on reload after an unload, so long as the ATs are on a hostile planet.
/end my 2 bytes
