What I would have done
As a DM: Reduced the level of the encounter a bit. It's just excessive for a 2nd level party. Maybe 4 skelletons and 4-8 decrepit minion skelletons, instead of 8 skelleton warroirs. That'd've made the skelletons a large force, but one that'd've been more dynamic to fight. With 8 soldiers taking up space and marking you, a fight is likely to get very static. If there's a story reason for 2 wriaths, fine, two wraiths. Still a very tough encounter.
Second, I probably wouldn't have had the skelletons just happen to pop out of the ground completely surrounding the PCs - that's a situational thing that makes the fight even harder. Rather, I'd have them emerge from the ground in cool-looking ranks, like they were a military unit, or burried in neat rows like a graveyard or whatever. Evoke a little Harryhausen. I might bring the wriath in first, have it taunt the PCs and order the skelletons out of the ground, or, have the skelletons rise, then the wraiths swoop in once the players dust a few minions or turn undead and start to feel less threatened.
Upon hearing the party would be down a PC, I'd cut the enemies apropriatelly, remove one of the wraiths and some of the minions, for instance - ideally, such that the exp/player remained the same. Suddenly, no more/less exp issues, either.
As a player:
I play a warlord in my current party, and he'd have been pretty unhappy with the situation, starting a battle surrounded is bad, and retreating into unexplored buildings isn't a great idea, either (could be more monsters or other hazards in there). I'd have made darn sure the Cleric's Turn Undead worked propperly, though - ignoring the imobilization made a pivotal power into a minor anoyance for the bad guys - the DM and the player should both know thier power, though, so I shouldn't /have/ to (but, in our group as in yours, the player of the cleric doesn't always remember his powers quite perfectly - in our case he's just a little more casual a player than some of the rest of us - it took a while for me to get him to remember that Healing Word was only a minor action, for instance). I've generally found turn undead to be underwhelming, but in this scenario, it'd be pure gold.
From what you said, it seems there were some initiative-related problems. The Cleric and Wizard aparently went right before the undead, who all shared an initiative. So they'd turn or thunderwave, and, the undead would fill thier ranks back in before anyone else could react.
From the player persepctive, that's an easy mistake to make, especially on the first round, when you don't know the enemy's initiative. But, it's something you have to get over, and one of those times to ready or delay to get more use out of the positioning power.
From the DM perspective, that's one of the downsides of running groups of enemies on the same initiative. You have 10 enemies, of only two types, so only one or two initiatives for them, in effect, then, they are perfectly coordinated by default, while the PCs have to work at coordinating thier actions. That's a natural advantage the DM has (just as being able to put more thought into individual actions is a natural PC advangate), but sometimes you need to compensate for it a bit. This'd be another reason to have more than one kind of skelleton - to further split up the enemy initiative. You could also have divided the skelletons arbitrarily (those nearer or further from the well for instance) to ge some different intiatives, and break up the enemy round a bit. Not having all the enemies go at the same time keeps things a little more interesting.
