I left a lot of questions out about how MJOLNIR armor works because I'm not familiar with that much of the Halo universe, however I am wagering that the suit has several electrically-based systems that an EC grenade would have an adverse effect on, and thus would have a negative impact on the Spartan's movement and function. Could Cortana take an EC hit? I don't know, but chances are she would be effected in some way (Maybe she'd be erased, maybe she'd just turn off for a while, maybe she'd start talking in Latin and dancing...chances are she would not be helpful during an encounter). I don't think even a supercomputer like Cortana would be able translate Mandalorian that fast; this encounter would be over in, what, minutes? I don't think she could crack their communication system, translate their system, and relay it back to the Spartan before the encounter was decided one way or another. Even humans require a healthy exposure to the language (Also remember not only are they talking in different languages, they're on different technology levels...Chief probably wouldn't understand what a DC-17m is, or what Pod Maneuver D-35B is) to translate it.
Do Spartan suits have a "surge protector"? Who knows. The Covenant doesn't seem to use a lot of EC-ish weapons, so it wouldn't necessarily be top priority. The Commandos don't have something like it, and the Star Wars universe is by far more technologically advanced than Halo's, thus chances are the Spartans aren't armed with one. Even if they did, the shield would still be drained out, which means a Spartan is going to die very quickly. Try playing Halo or Halo 2 with your energy shield down and have a grenade go off on Chief; see how he handles that. A lot of their durability comes from that shield, and when it's gone, a Spartan is a whole lot less resilient.
As for their specialties, the clones are genetically engineered to be masters at every craft of war. Humans are not designed, at our foundation, to be war machines. We each have varying interests and skills that are spread out in various fields; a soldier good at one thing is not necessarily great at another. Just because you're awesome with a sniper rifle doesn't mean you know whether to cut the red wire or the green wire.
In 15 years, the Spartan probably still does not have the knowledge that a Commando is born with. It's spliced into his genes. Also, as I said before, a Spartan is probably exposed and trained most to fight Covenant, and maybe humans. Commandos are trained to fight humans, droids, trandoshans, Wookies, and any other of a baker's dozen of races in the Star Wars universe. That means they have a lot more tactical knowledge and a lot more tricks in their sleeve than the Spartan does. Regardless of how one performs alone in their respective games, that's not what this discussion is looking at. The question isn't can a Spartan kill Covenant faster than a Commando can kill Geonosians. We're comparing one against the other, which doesn't have much to do with how fast they kill in their own games.
On a standard mission (Where I compared the Spartan and Commando), odds are he wouldn't be equipped with a sniper rifle. Generally when you have a sniper rifle in Halo, it's because you picked one off the ground, not that you started the mission with one in your inventory. An assault rifle/shotgun is more tactically sound than a sniper rifle/assault rifle. That makes you effective at everything except very long range, but even if a Spartan DID come with a sniper rifle, he's still outgunned by the Commando. The Katarn armor and energy shield could take a hit from a Halo sniper rifle; the same can't really be said for a Spartan without an energy shield taking a hit from the DC-17m's sniper attachment. Plus, the Spartan has surrendered the one thing that really made him more dangerous in close combat (Where he would have an advantage on the Commando) to focus on ranged combat where the Commando has him outgeared.
To me, no matter how you cut it, without the Spartan getting into close combat he has no chance to beat the Commando. In close combat he'll undoubtedly win most of the time, but most of the time he'll never get there. My bet stays with a Commando, who can negate every advantage a Spartan has at ranged combat, while still maintaining technical and tactical superiority.