The problem won't be so much with some trying to disqualify females as it will be that after qualification females will get shuffled into lesser priority positions within the higher priority units. In Special Forces for example, it's long been said that it takes 6 years after the initial qualification course to make a good Special Forces soldier. There's mandatory cross-training in a second SF specialty (cross-training in a third SF specialty for SF warrant officers), training in one or more foreign languages, military free fall, scuba, various survival courses, SERE, SOT ... etc. On top of all that, Special Forces teams are area specialists who've done country studies and are continuously updating them with concentration on their specific area of operation.
How do you replace someone with all those capabilities and specialized knowledge if you have to deploy an SF team; but, one of them is pregnant? You don't. You may be able to put another warm body with the basic qualification on that team but it won't be as effective and they all know their lives depend on that effectiveness: they're not a sports team. It used to be up to chance that someone might become non-deployable because of something like an accidental injury. Now they have to plan on it being a deliberate act.
It doesn't cost them anything in terms of deployability to put females through a qualification course; so, I think where they'll be getting really creative is in how they assign females afterwards even to the point of creating low priority teams around them depending on the individuals they have to accommodate.
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