Based on the fact that this conversation is even taking place, and the fact that Samus has not made her feelings about the Metroid hatchling known outright until this point, it's VERY clear that the situation was ambiguous up to this point. The fact that Samus gave the hatchling to the science federation could just be justification for her actions. You could look at it a lot of different ways. That's what makes it ambiguous.
It
was ambiguous. I'm not debating that. The point of this conversation is to discuss whether or not events were contradicted and/or retconned. The creators made it a point to be ambiguous in Metroid II and leave Samus' feelings up to the players and they could have easily remained ambiguous in Super Metroid, but they made a conscious decision to offer an explanation which makes Metroid II's ending not ambiguous anymore.
You could argue Super Metroid, retconned Metroid 2 if you want to go there then which made it quite clear she felt sympathy towards the baby hatch-ling and didn't complete her mission, which wasn't to capture one but to destroy them all. The end of Metroid 2 seemed to heavily hint at the fact she felt sorry for the creature, and chose to let it live going against her orders, indicating an emotionally based choice.
I didn't say Super Metroid didn't retcon Metroid II, but if you really want to get into it, it does. The main difference being in Super Metroid, she points her arm canon at the hatchling which she does not do in Metroid II. Doesn't change much since she still tells us her motive, but that's retcon by alteration since something different happened than what was previously established however subtle it may be.
You say Metroid II made it quite clear that Samus felt sympathy toward the Metroid hatchling. Well, clearly it didn't because Super Metroid tells you her motive. I'm strictly going by what the games specifically tells us. Something is no longer left up to interpretation when you're flat out told what that something means. Again, it
was left up to interpretation and now it is not. Unless you want to get into the intricacies of unreliable narrators (though we have no reason not to believe Samus) or a philosophical discussion on the nature of truth or the lack thereof, Samus' motive and feelings are made perfectly clear in Super Metroid though that's not to say Other M or another game won't just retcon that and specifically state that Samus felt sorry for the Metroid hatchling. However, as it stands, Samus did it for science.
Also we know nothing about Samus's demeanor in Super Metroid after the Metroid died, she had no time to grieve since the whole flipping world was about ready to blow up.
Yes, exactly. The ending of Super Metroid is once again ambiguous and left completely to interpretation. That is, until Fusion where it's still ambiguous, but less so after Samus makes that comment about the hatchling saving her (which, for consistency's sake, still has no bearing on her feelings prior to being saved). She didn't grieve, but did she not grieve because there was no time or because she didn't care? In Super Metroid, we don't know. In Fusion, we know more. She cared enough to acknowledge that she owed her life twice over to the Metroid hatchling.
/long post