Do you play on v2.6?
On v2.5, I'd bet on 1 rocket launcher, 2 machine guns, 2-3 flame throwers on reaction fire (at least one per hot spot; no alien survive a reaction fire in early game, save the Ortnok), snipers and the rest with assault rifles on controlled fire more (even a rooky can get up to 2 chances out of 3 to hit something), ... and smoke grenades.
However, without any armour, your troopers are likely to be one-shot if they are caught outside of the smoke cover.
Of course, the transport hangars are on the other side of the entrance, and there's a nice "death" corridor between my men and the entrance. Beware the non upgraded radar tower, as it attracts a few aliens (consider it as compromised if next to the entrance, I mean perhaps one Shevaar would have preceded your men in the stairs). Also the first time your main base (first base) is attacked, it's likely that it's not restructured yet: the workshop makes a nice "back door" to make the final swipe quicker and safer.