Marathon always was harder than the standard game, due to the longer research times and wound recovery, and higher costs. The trick with Marathon is that, unlike standard mode, you have to build laboratories and take scientist reward missions as priorities.
It's the way back that's a problem. However slowly you move the survivor, you get two spawns on the first turn, three on the second, and two on the third, and they mostly don't spawn in sniper-friendly places (as well as spreading out too much for explosives). The mission is in early April, at which point you aren't guaranteed to have a squadsight sniper at all because soldiers promote a lot more slowly in EW. Any alien that survives its drop is likely to head for ground level in its first turn of movement, where it can easily flank the survivor because the ruined buildings have exposed interiors.
En route you can also trigger a couple of the aliens - particularly the one at the back of the map - when they're too far away to easily hit (and well outside explosive range) and that alien particularly can hide behind the vehicle, where he's quite difficult to dislodge. Of course you also can't avoid triggering the 3 central Thin Men together (at least, you can trigger the one on the roof first, but he'll instantly move out of sight so he'll still be alive when the other two activate), and being faced with two Thin Men at close range with low-level soldiers will usually mean some fatalities - I got round that one with a flamethrower, for which I obviously needed a MEC.
Which takes a bit of luck unless your heavy has better-than-average aim. I had my overwatching Support to deal with that Thin Man; his shooting dealt 3 damage and he went down next turn. To keep the Support alive I had to run the MEC back to deal the final point of damage before he bled out (since as per usual for Council missions you have to kill all aliens to win the mission).