The covies would likely enter a civil war arising from debate over whether to worship or attack the reapers. The Covenant could destroy the mass relays to stop the reapers from traversing the galaxy, however that would also probably be considered 'blasphemous and heresy'. Also, doing that doesn't actually kill the reapers, just immobilises them. Also also, ME Andromeda may see the invention of FTL travel without mass relays needed. An individual reaper could take out multiple Covenant ships before being destroyed, however their numbers are likely a bit smaller and the covenant's largest ships are massive in comparison to the reapers. The reapers however have indoctrination, which is what I think would grant them eventual victory. Imagine the havoc they could enact on the Covenant if the prophets were indoctrinated, and 'weak' species like the Uungoy and Kig-yar are likely very easily turned. Reapers can also convert deceased corpses into combat forms, not too dissimilar to the Flood actually. This would turn the Covenant's strength in numbers against them. Glassing by plasma bombardment could probably kill a reaper pretty easily and effectively, however using that as a weapon is probably quite unreliable in most cases. I think Covenant shielding technology is also more advanced too. The reapers also have the collectors on their side let's not forget. However the Covenant would be pretty capable of dealing with them I think. I'd give this a narrow victory to the reapers. Narrow, however.