The Covenant ships require hours to destroy a planet surface, and people overestimate the power of these weapons. At the speeds that they supposedly travel, and the time it takes for these weapons to hit there targets, there would be a noticable delay between the position the crew of the ship think the enemy is in, and the position they actually are in. A simple, random evasion pattern would cause the Plasma Torpedoes to overshoot, and I doubt that Plasma Torpedoes (despite the obvious retardness of this statement) can turn around and continue at the same speed. I hope some people realized this...
The Covenant may have thousands of ships, but how many of them can stand up to a ship like Enterprise?
forgive me, but I'm working off of memory, so you're just going to have to settle for me doing what the Star Trek side does: giving little to no reference data, and few measurements that are known. I do note that Josef did provide a good amount of references, tho
1) The Covenant Plasma Torpedoes can easily turn around on their earlier course, retaining their previous speed. This is due to the fact that they are not fire and forget weapons, like phasers, and are guided by magnetic field manipulation. this is the source of their speed. This was demonstrated by Captain Jacob Keyes, who first performed the Keyes Loop (I believe this was mentioned in First Strike, but can't be sure) in the Battle of Sigma Octanus IV (http://halo.wikia.com/wiki/Keyes_Loop).
2) to be able to completely crystallize a planet's surface in a matter of hours is no mean thing. planets are big. they have huge amounts of surface area. and even a fleet of two-three hundred ships (standard combat fleet size for the Covenant) of five to nineteen kilometer long ships will not cover very much space. Earth, a relatively small planet, has approximately (If I did my math right) 6966331437.57, 7000000000, or 7x10^9 square miles
3) there have been thirteen fleets mentioned in the Halo series, all of which involved in the war on the UNSC, most of which have two to three hundred ships each. The Second Fleet of Homogeneous Clarity consists of at a bare minimum 2.5 thousand capitol ships, with uncountable strikecraft. there must be many more fleets behind Covenant lines, maintaining order and garrisoning their worlds, should a rebellion or invasion arise.
4) The standard MAC gun, equipped on nearly all UNSC frigates, cruisers, and capitol ships, delivers a 600-ton projectile at a muzzle velocity of 600,000 mph. this results in 360,000,000,000 joules. that's 360 gigajoules of force
The "Super-MAC", mounted on orbital MAC defense stations, and theorized to be mounted on the UNSC Supercarrier delivers 21.6 zettajoules of force, or 5867.5 Gigatons of TNT. This is from a 3,000 ton ferric-tungsten round with a muzzle velocity of approzimately 40% the speed of light. (http://halo.wikia.com/wiki/Magnetic_Accelerator_Cannon)
5) Covenant ships are also armed with two other main weapon types: the Energy Projector, and the Pulse Laser Turret. The Pulse Laser Turret (PLT), seen in Halo: Combat Evolved in use against the Pillar of Autumn, is a commonly mounted weapon on Covenant ships, ranging in size from the handheld Beam Rifle, much like the human SRS 99D AM Sniper Rifle, to large scale anti-capitol ship weapons capable of melting through at least 45 centimeters of Titanium-A armor plating in a single shot. being a laser, this would pass through any Star Trek shield, as they are transparent. (http://halo.wikia.com/wiki/Pulse_Laser)
The Energy Projector is a weapon mounted only on Covenant capitol ships, due to power constraints, and is the weapon used to "glass" planets. it is both an antiplanetary weapon, and is an anti-ship weapon. It has a range of at least 50,000 kilometers, exceeding even that of an orbital MAC gun, making it a long range sniping weapon that is absolutely devastating.
when used in ship-to-ship combat, a single shot can remove a ship from combat by destroying its weaponry, disable a ship, or completely destroy a ship, with a single shot. They have been observed to "gut a ship from stem to stern in a single shot", such as the frigate Gettysburg in the Battle of Reach. Its size is variable, thus its power is also variable. it can be focused into a pinpoint, giving it insane amounts of power, and the ability to carve a ship apart, or can be expanded to cover square miles of land
6) The Nova bomb, which is nine fusion warheads encased in lithium triteride (from here on reffered to as LT shell), has huge destructive potential. So much, that is literally a planet-killer, and is nicknamed as such. loosely calculated, it has a 27 gigaton yield.
this is because of a) nine fusion warheads, assumed at 30 megatons each; and b ) the LT shell reflects the blast in upon itself, thus increasing the strength a hundredfold and compressing the core to neutron star density
and 7) Inertial dampers are used by both sides of the Human-Covenant war, most extensively by the Covenant. The Covenant use them both for utility and for show, as evidenced by views of water flowing up, down, and sideways. this is reffered to as gravity manipulation, as well as inertial damping.
beware the ninja cylons!