Putting the valve before a pump can lead to a pump running dry and cavitation. This is more of a concern when you completely shut the valve. While your configuration isn't ideal, I think you should be fine as long as you don't shut it off or get really close to shutting it off. Most aquariums pumps don't have a high enough inlet suction pressure to create much cavitation, so you can probably go fairly low, but if it does start cavitating, you'll hear it real quick.
No way to swap the valve position?
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