You've probably gotten this comment alot aleady Just_Darrell, but I thought that that was a great post on your part :-) I totally agree that the Commandos 1up the Spartans in firepower and more tactical options available in the equipment that they carry. I'd have to question your Spartan's tactics in your scenario though (wouldn't exactly go bum-rushing a heavily armed alien soldier whom I knew nothing about, throwing what clearly looks like grenades at me.)
In your scenario, I feel that a savvy Spartan would have more tactical options at his diposal than you make clear. One is that you armed your Spartan with an M6D pistol (you said 'pistol', I know, but i figured you were using halo 1 weapons procurment in that you mentioned your Spartan having an Assault Rifle.)
M6D pistols are issued with 2x smart-linked scopes that feed the visual data to the Spartan's helmet. It fires 12.7mm semi-armor-piercing, high explosive rounds. In Halo, it is a potent weapon that is deadly at close, medium, AND long ranges, in skilled hands. Covenant Elites wither under pistol fire, shields and all, in just a few shots to the cranium. It's one of the most versatile weapons in the game. In your scenario, I feel that a Spartan,ducking out of cover with the pistol and firing at the Commando's head, could kill or severly wound the Commando with just a few hits. It gives the Spartan a fighting change going against the Commando's DC-17m sniper attachment. It takes time for the Commando to switch weapon attachments in the heat of battle too. Not overly long, but long enough to be fatal.
The Covenant (or the Commando) may be blessed with superior technology, but as the saying goes, If it hurts, it works. Stormtroopers lost to little bears with sharp rocks and pointy sticks after all :-)
Another thing that I'd like to point out is that The Spartan has more than a chance of dodging blaster fire. And that blaster fire isn't very tactical at all. All the weapons that the Commando utilizes in battle (save for the sniper attachment and the gauntlet blade) fire in discrete bolts. You can see grenades sail through the air, you can see blaster bolts from the point they leave the blaster to the point where they hit something. In that way are the MA5B Assault Rifle and the DC-17m not equal. Damage caused by the Assault rifle is nearly instantaneous due to the high velocities of the projectiles fired. It would be very difficult for the commando to score hits on a super strong, super tough, super quick Spartan at medium-to-long ranges using standard blaster bolts, due to the lag time of the bolts. Furthermore, because of both the lag and the shiny nature of blaster fire, blaster fire of any stripe will give an opponent like the Spartan an extremely good fix on the commando's position.
The last point I would like to make (not a very big one though) is that the Spartan has a really good throwing arm. Next time you play halo, try arcing at 45 degrees and letting a grenade fly. It flies for like a hundred yards. Now it's just a hand-thrown grenade, right? would it be useful to the Spartan at medium to long range? Most likely. As you said, Humans in Halo are trained to fight the Covenant. One of the fastest ways to dispatch a Covenant Elite is to throw a sticky plasma grenade and make it latch to the elites armor. A Spartan would be trained to throw very accurately over long distances. So I feel that grenades are a viable option for the Spartan when combating a Commando at medium to long range.
Yes, more than likely, the gear that the Spartan carries with him into battle will not be as tactical as the gear a Republic Commando is accustomed to carry. But the Spartan's gear is built to be versatile. It's what allows the Spartan to take on jobs like capturing Covenant assault carriers single-handedly, and repelling alien invasion forces fifty times his size on foot with an assault rifle and a handful of grenades.