I take my decision based on the info the game provides. The squad-mates certainly know more than the player, and one of them will always suggest that you wait.
In retrospect, during a replay, or knowing spoilers in advance, I do know that saving the council will be the right choice, the happiest ending, specially in the long run since it will improve humankind´s relations with other species, while at the same time advancing Earth in terms of power politically and diplomatically, even though the alliance will still suffer bigger losses militarily. But then, you don´t have to take a guess. There´s no risk involved, and the only reason why you still get a happy ending is because of an arbitrary decision by the writing staff.
In a blind play, however, based only on the info the game provides, with no foreknowledge, waiting for a shot at the reaper seems like the wisest choice (and it doesn´t have to be cruel).That´s what I would have done if this was a real-life situation. After all, the councilors themselves told me that: 1-The success of the mission was paramount. 2-Sometimes you need to make sacrifices for the greater good. 3-They had no problem in wanting me to exterminate the rachni, an entire species. So what, If I let a few thousands of asari to die in the DA as well as 3 moronic fools whose incompetence allowed this tragedy to take place when my character could have prevented if they did not try to sabotage and discredit him in every possible way? 4- They did not care about the human colonists, they did not care about the rachni. 5- The turian councilor even dare to insinuate (actually, it was a clear accusation) that my character jeopardized the mission while trying to save innocent controlled human colonists, and that I would go to any lengths to help humans. My shepard learned the lesson well from them, so now they can have a good taste of their own medicine.
It wasn´t malevolence. I would have saved them, however, if I could know for certain that it was safe enough to divert human forces to eliminate the remaining geth and still have sufficient firepower to subsequently take down this gigantic dreadnought of unknown configuration likely to have immense defensive and offensive capabilities, and also do it fast enough before he/it can bypass the citadel controls and fill the sky with a few hundreds (and that´s being optimistic) of his friends, the army of sentient machines with a large track record of exterminating advanced galactic civilizations multiple times... There´s no room for mistakes here. If I waste resources now, and can not bring the reaper down, all hope is lost, not just for humanity, but for every advanced species in the galaxy in this cycle (and possibly others to come). There´s only one shot, so it has to be my best possible shot. It´s not much different than medical triage.
Frankly, I don´t even know how this matter can be polemic. Same thing goes for taking the collector base. If people hesitated to take it for fear that their equipment could indoctrinate people (well, we could always send simple remotely controlled robots now that we have the omega 4 relay) I could understand their reservations. Indoctrination could pose a really big dilemma. But merely because it was tainted by innocent blood? Oh, come on! Can you imagine the police destroying, out of repulsiveness, important proofs taken from the lair of a serial killer in the form of annotations, film recordings and computer data that he had about torturing his victims? Or an international committee doing the same with info collected on a Nazi-prison camp? This whole reasoning of "abominable things happened here, so we must wipe everything out till no trace remains." is totally bankrupt and dumb. If one really cares about the colonists, then this person would try to salvage as much material and data as possible from the base and try to learn all one could about what they did, how they did, and why.
If my shepard had unnecessarily and irresponsibly destroyed the base, not only he would have eliminated precious evidence about the barbaric atrocities by the collectors (that could help save lives), but this would be nothing less than a negligent crime by itself. It´s irrational.
I´m glad that there´s a way to let the council die (or better yet, leave them to their own luck and the fruits of their poor judgment, since they never counted on Alliance support anyway) without sounding merciless or sadistic. I don´t think it is a coincidence. It´s the place in which the lines of renegade and paragon converge. It´s common sense. You make the right tactical decision, but without being guided by evil emotions of revanchist sadism trying to make them pay for what they did to you without ceasing to be noble nor heroic.
One can be innocent as a dove, but wise as a serpent. In real life people can be sensible, kind, altruistic, charitable, caring, decent, honest, and yet having the courage to make tough choices while being realistic, as well as being nobody´s fool. One should be able to play paragon without being dumb.