Rachni are just sooo maternal. ME1 "I would have ended them myself." Rephrased: "Mom - If you don't listen to my lullaby, I'll eat you." She's just bartering for her own life. As Queen, she orders he subjects absolutely... doesn't have to convince of anything. Wrex holds power only because the other Krogan allow him to hold power.
Then there's the "Reapers made me do it" explanation for the whole situation as to why they just didn't disappear and stay in hiding after ME1. Yeah, a real history of living up to a promise, eh?
Not to mention that we're expected to believe that the Queen became the quintessential example of Rachni stability... even though "she was just an egg" who was apparently not listening to her mother's soothing lullaby, but hearing her cry and listening to songs like "oily shadows" as her entire race was being exterminated. As for rapid breeding... makes the Krogan look like they're doing it in slo-mo. "entire colonies within days" and apparently without the need of any sexual partner at all. In the time period between Shep saving her on Noveria and the encounter in ME3, rachni numbers should have easily far exceeded the Krogan and Turians combined.
Under the circumstances, the only choice Shep can make is to spare her, take her on as an ally rather than an enemy... and hope she keeps her word this time around... or wind up fighting both the Reapers and the Rachni kids (for slaughtering their Queen) at the same time.
Rachni are 'alien' to pretty much anything else in the series, but that doesn't mean they lack any form of maternal care. The test subjects are pointed out as being insane; as Garus puts it: "Like keeping a kid locked in a closet until they're a teenager." The Queens have command over the other Rachni castes, but there is a social development process that is involved (the singing) which would indicate that they actually do care for and raise their young in some capacity; just not in a perfect 1:1 comparison to humans. Also, even with the Queen being in command of the other Rachni, she recognizes the harm that her species caused; Wrex, as an individual, won't acknowledge that about the Krogan.
As for living up to promises, even if the queen was just bartering for her life on Noveria and all she was just going to do was to hide away once freed, why would she send an agent to specifically hunt down Shepard on Illum to tell him/her that she was still around and that she hadn't forgotten about her promise of aid for the galaxy? There is no way Shepard (or favorite writer's pet Cerberus) could have known that the Queen had an Asari agent working for her so why would she reveal herself like that if she had no intention of helping in the fight against the Reapers? The Rachni could have quietly drifted off into the shadows, riding out this cycle's harvest in safety, and no one, not even the Reapers, would have been able to do anything about it; the Rachni survived the Prothean cycle's harvest just as easily. The fact that she directly contacted Shepard, and revealed her existence to him/her as well as Cerberus tells me that she was actually going forward with her promise of aid.
Flash forward to ME 3, and the sheer amount of Ravengers encountered in the field points to the fact that the Queen was building up quite a sizable force. Now, if you want to assume that she only intended to use those Rachni to wage war on the rest of the galaxy, then I would again have to point back to the scene on Illum and ask why would reveling one's presence, as well as their intention of building up an army, make any sense if they were just going to attack us all? The smart thing to do would have been build up in secret, and then ambush the unsuspecting galaxy with your forces, not tell people about it.
The Queen specifically mentions how the Queens are naturally more developed and/or resistant to deal with the silence compared to the other Rachni, and even if she was just making that up, the fact that she is communicating would speak volumes to her being more "stable" than any other Rachni the galaxy has encountered previously; in the present or 2,000 years ago. Her position as to how the insane test subjects must be euthanized is just being merciful on her part, they are suffering and are a danger to others. At the very least the Rachni are pragmatic about their young; the Krogan would try and save every one of their children, regardless of any potential dangers they might pose.
This also shows that the Rachni are quite capable of population control, of intentionally thinning out their numbers should the need arise, something the Krogan seem to be unable to do without outside assistance. Just look over the lore surrounding the Rachni Wars compared to the Rebellions, worlds were able to be retaken from the Rachni and then resettled; whereas the Krogan just left environmentally devastated or completely un-inhabitable planets in their wake. Even being mind controlled, the Rachni are demonstrated to be better managers of their holdings, and not completely wrecking them via uncontrolled population growth like the Krogan. If you want to see what the 'regular' non mind-controled Rachni are capable of just look at the lore surrounding the Rachni home world of Suen, massive towers of impressive, near space age level architecture, and not one mention of a self-inflicted nuclear war.