I don't believe the capital-C Combine hate the race of Vortigaunts, in fact I'd imagine they consider them 'just another' race they've enslaved. The reason why they're given such menial roles and kept on such a tight leash like we see them on Earth is probably due to their abilities making them so dangerous, unlike humans who aren't exactly much of a threat if they aren't armed/organised, which is why they're constantly transferred place to place on the regular.
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