good guys point guns at bad guys. bad guys point guns back and explain "we have a team watching us. if anything goes wrong they will detonate the bombs we placed here which will destroy a whole city block."
ok so the good guys have 2 choices. defiance or appeasement. now i don't want to take anything away from the defiance option, but in the specific case i believe it was credible that if they let bad guys leave, they would not detonate bomb anyway. also it was pretty credible that defiance meant boom.
and of course since Alias is kinda wussy, appeasement it is. so you expect bad guys to back out while still being aimed at. but instead bad guys demand good guys drop guns or boom.
ok now again defiance or appeasement. but now if you say no, bad guys have nothing to gain from boom. they aren't facing death or death. they have the choice between killing themselves or leaving. and all they have to do is endure having guns pointed at them a little longer. so defiance looks like the good bet.
but of course since Alias is a kinda wussy show, they went with appeasement. good guys dropped their guns. this is idiocy. now bad guys can shoot whoever they like before leaving. and in fact in the show after good guys dropped guns, bad guys decided to take one hostage and bring her with them. that wouldn't have happened if good guys kept their guns.