The Covenant have no psykers, only the Flood and the Overmind *cough* I mean, the Gravemind utilize anything approaching telepathy.
I think a Scarab would be about the equivalent of a Warhound Titan, but laughably under armed in comparison. So a smallish Titan Legion could likely lay waste to just about anything the Covenant could throw at them on the ground, even the entirety of the Covenant armed forces in a combined effort. Titan Legions are few and far between however, so probably not worth considering so long as the Covenant steer clear of Forge and Fortress worlds (which they may not be particularly won't to do). Actually, the Covenant on the whole are rather lacking vehicles wise, even if you include stuff from Halo Wars. I mean, that's more or less what you'd expect from an FPS centered franchise, but given that their standard vehicles are mostly light skimmers and the equivalent of jetbikes . . . I'm beginning to think you wouldn't need much more than a well armed and equipped Imperial Guard Chapter to defeat them, especially if they could deploy say, a Baneblade or other Superheavy Vehicle.
A Baneblade would be more than a match for a Scarab, or two, or three, so while I'm willing to give the Covenant a few victories over planetary and system militias and defense forces. A few concurrent victories is all you really need before the Lords of Terra decide it's time to raise a new IG chapter and finish off the Xenos threat before it becomes any more of an annoyance; or if you're really unlucky, a Space Marine chapter will answer the call, and as you pointed out, the average Space Marine is more or less a match for most of Master Chief's escapades (minus the plot armor) so it doesn't take much to imagine what a Terminator Company would due to the Covenant Armada piecemeal.
I hadn't even considered the difference in scale on the space level . . . I was busy factoring how much faster Covenant ships would be in and out of Warp Space. According the Halowiki, Covenant Cruisers, the mainstays of their fleets range between 300 and 3,000 meters in size. The Covenant heavy hitters like the less than common Assault Carriers can be as big as 5km, and the Supercarriers (of which 2 are mentioned anywhere in the series) are a whopping 29km bow to stern. Destroyers and Frigates make up the bulk of the fleet (maybe as much as 2/3rds) and are smaller than 1km in size.
Compare that to the workhorses of the Imperium of Man, the Lunar Cruiser, 5km long and weighing in at nearly double the tonnage of even the largest Covenant cruisers. Now the Covenant are able to field hundreds of their own cruisers as the backbone of their fleet, but the IoM fields 600 Lunar class cruisers in the Segmentum Obscurus alone. That's on top of the Dictator, Dominator, Tyrant, Cardinal, and Gothic class cruisers which make up nearly as many again! That's twelve hundred ships, each of them larger and better armed than a Covenant Assault Carrier, the largest normal class of vessel in any given Covenant Fleet (serving as flagships). Imperial Heavy Cruisers and Battleships are even bigger, better armed, and outnumber their counterparts in the Covenant Navy, maybe 10 to 1 in any give Segmentum of the Imperium. Perhaps most tellingly of all? Covenant weapons appear to have an engagement range of of a few thousand meters, that's missiles and beam projectors and other plasma weapons. The smallest vessels of an Imperial Battlefleet have gun batteries and lance weapons which measure their effective engagement range at tens of thousands of meters. Covenant craft won't even be able to get a shot off against Imperial Craft until engaging them at what any Imperial Captain would consider 'point blank' range, the range at which they'll be launching apartment building sized artillery shells at ships less than half their size.
I'm calling it, haha, I can't imagine how the Covenant could possibly survive if they can't even tangle with a small battlefleet without sacrificing half their armada.