The plot thickens...

The thing here is, I'm almost certain that wasn't what Alphonse was going to say (I assume he wanted to say something about how trying to bring back Trisha wasn't comparable to this at all... I'm reminded of 12-year-old Ed with Tucker)

But a not unfair point is being made in the context of the military/Ed and Al's involvement with it. Thus far, the Elric brothers haven't liked the military, but as such have seemed to feel that their being tied to it (and appropriately disliked) for each other's sakes is a necessary sacrifice/a mature choice (as I've said before, they seem to view maturity/kindness as equivalent to ignoring your own wants or needs for someone else).

But I think when Lust equates sacrificing the prisoners with Ed being a state alchemist (and Al having wanted to be one), it puts things in a bit more perspective for Ed? Because Ed + Al are far from the only people at risk here... It's not just about their lives, it's about the people who the military is actually targeting-in this specific instance, these prisoners

So Ed refusing to follow orders with this in mind (even when Al was on the line) was probably the primary reason why Scar chose to help him escape (though ofc Scar seeing himself and his brother in Ed and Al was also part of it)