As others have noted, it depends on what the contract says. When I was working, we often had a significant number of 'contract' engineers. Boeing liked contract engineers because they were easy to hire or let go, and so they could respond to variations in workload without adversely affecting the core workforce. Some of the really good contract engineers were made offers and became direct employees - many others we were just as happy to seen gone when they left.
One of the terms of the contracts was that either side could terminate, at any time and without cause, with 2 weeks notice (no notice required if the termination was 'for cause' - e.g. theft).
About 20 years ago, our division chief came out of meeting where he'd been told he needed to cut costs and announced all contract employees in the division were given their 2 week notice, effective immediately (at the time, roughly 10% of the engineers in the division were contract). Given the circumstances, coordination and transfer of tasks from the contract engineers was all but none existent - in fact many simply stopped coming in. Although the reaction of direct employees was near panic, it turned out that by most metrics (e.g. on time completion of tasks) things actually got better after the contractors were let go.
If the pilots contracts are similar with provisions that either party can terminate without cause - and a pregnant pilot can't fly - then it's perfectly reasonable for the employer to say 'if you can't fly, you're terminated'. Sure, it sounds bad, but if you're under contract to do a job, and you're no longer able to perform that job, then most people are going to be be let go.