Work around: use a 2x2 source. No single block loss will kill it.
If you want double redundancy, use a 2x3.
I thought about that, but the layout of my set up doesn't make that ideal.
I figured out that the pump for some reason tries to grab the block below and 1 block to the east of it first, so I just offset the 1x3 by one block to the east.
Is this a bug or working as intended? If a bug I'll file a report in the tracker.