Tactically ignoring the Ascension makes no sense. The Alliance fleet has surprise and is attacking the static Geth force from (effectively) above, this means that they have the speed advantage which in air combat (and presumably space) is a really big deal. Basically they're position to swoop in and wipe out the Geth force with minimal loses.
The alternative, is move past the Geth force and into a confined space to engage an unknown enemy. This means that as soon as they engage Sovereign the Geth fleet will be behind them firing from a spread out position in on fleet packed into a tight space with nowhere to move. That's suicide. That's Persians at Salamis levels of stupid.
I'd say sacrificing civilians to save soldiers is missing the point of having soldiers as well, but that's another discussion.
(edit) Not that I'm saying your wrong, I just disagree with how the game frames the choice, or that it is a choice.