Actually, think about it.
How large really is the Covenant?
If one says that the Covenant was toying with the humans, I would disagree. Seriously, Truth's power was entirely reliant on hiding the Truth about the humans and Forerunners (whether you think they are related, or related figuratively, is up to you). He would quite desperate for the entire annihilation of the human race. So why not make it quick, and take the entire Covenant Navy to the fray?
There are some explanations. Before the split, much of the Navy may have been diverted to examining and protecting Forerunner artifacts (seeing how 'crude' and 'savage' the humans are). Considering that Alpha Halo was the first Halo discovered, and Delta Halo the second, this would mean that the Covenant is probably not galaxy-spanning (seriously, giant Forerunner artifacts elude Covenant 'artifact scans'?), most likely not even close to that.
After the split , there would be the Flood and the Elites against the Covenant empire, so it would be preoccupied and unable to bear its full might against the UNSC. Well, there's a lot of time before that, and where did the Covenant go during all that time?
Also, think about the number of ships that would be lost during the split. It is unlikely that by the time of Truth's genocide of the Elites, the Brutes would taken the extreme majority of the Covenant fleets (more than 80%). The Elites would definitely smart enough to notice the ploy were it to go that far. Even if the Brutes did not have numerical superiority, thinking of how devastating Covenant weapons are against Covenant ships, it would not be surprising that the first volley against unsuspecting, possibly unshielded Elite vessels, would be able to wipe out huge portions of the Elite forces.
Also notice that Truth spent a while to reform a fleet of 500 ships, which means some supply strain, which implies they are busy somehow. Also, even after the fleet is decimated to a dozen or so ships, Truth does not ask for any reinforcements (although that may be because of the presence of the Forerunner Dreadnought). And considering a fleet of ten Elite ships designated as the Fleet of Retribution were outnumbered only three to one. That isn't a lot (ahem...300 ships at Reach, 500 in each of two fleets to purge Earth...). If that's the best they can do (which it isn't), it would be very...disappointing to say the least.
It is also likely most supercarriers have been destroyed or otherwise incapacitated by this time, as they would be a chrome finish for the death of Earth.
Oh, and by the way, High Charity's only one third the size of the third Death Star, and only twice the size of the first, which sort of shows that the Covenant may not be as powerful as one may expect (seriously, the Death Star in ROTJ was only around four years old. Seeing that as the crowning Jewel of the Covenant, it is unlikely larger Covenant battlestations existed.