In the fridge, an hour should not be a problem, but could still end up bitter depending on the kind of onion used. Usually, Marinades, Pestos etc. that use mashed onions and/or garlic taste best if they are made the way the name "Pesto" suggests: Cutting stuff very fine, then using a mortar and pestle.
Most explanations WHY that is the case have to with the fact that blenders tend to disintegrate cell walls with relatively rough cuts of a fast but half-sharp or blunt blade, releasing more enzymes etc. from the cell walls as opposed to from the cell contents. These are plausible, since some of the compounds in different parts of onion cells are known to actively react when the onion is disintegrated.
Also, try adding oil (which you often want in a marinade anyway. No unrefined olive oil in a blender, though - that is known to get bitter!) while mortaring or blending - this will help extract flavor compounds and probably provide some oxidation protection.
There is a well known marinade working with onions, garlic etc: Bulgogi marinade.