The house’s primary defenses have been activated. She’s probably still
suffering the side effects.
So the gas that was released was the primary defense, it would appear that was the best solution that the Red Queen had.
The Hive has its own defense mechanisms are all computer controlled.
You and your partner were intended as the first line of defense in the
mansion. If you were killed or incapacitated, then the computer could
deploy its own defenses. A nerve agent released through hidden vents
in the house. Primary effect of the gas is complete unconsciousness,
lasting anything up to four hours. Secondary effects are varied, but
can include acute memory loss.
The fact was that there was an outbreak, so them being the first line of defense had failed so the computer used all primary defense mechanisms available, i don't believe it intentionally targeted Alice, but deploy all primary defenses to prevent an outbreak.