Cathar,
No material expert here, either. In going through my book I find that the electrode potential differential from copper to silver is ~0.5V, copper to chromium (stainless surface chromium dioxide) is ~1V, and copper to aluminum is ~2V. All this is at 25°C.
From what you described of that pump, I'm reasonably confident it was a matter of contamination. Nonetheless, if contamination is likely in a typical system then I'd agree stainless ought to be avoided, especially in extremely narrow passageways.
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