I would not use non-metallic conduit if that's what you're asking.
How was the MC cable deteriorating? Was it exposed to the exterior on the roof? I've installed make-up air (MUA) units and they typically have a factory-wired power drop consisting of conductors sheathed in aluminum flex conduit (similar to MC). But those drops are intended to be fed through the roof within the MUA's equipment curb so they are not exposed to the weather.
Typical MC cable is not rated for exposure in wet locations; you must use MC cable specifically listed for wet locations. But I would not install MC cable of any kind exposed on the roof because it would be subject to damage from anyone walking/working on the roof.
IMO, EMT is the minimum that should be installed on roof tops. But for flat commercial roofs, I only use rigid conduit for exposed work on the roof. I've seen too many damaged EMT conduits from workers stepping on them, tripping on them, lifting equipment over them, etc.