We can distinguish them because they are pronounced differently, and "-ed" is past tense. I don't see what is confusing about this.
Edited to add: I see that I may not have addressed part of your question. You wrote:
Native speakers pronounce both sentences so that we just hear one [d],
so we don't know the tense by pronunciation in these cases. Am I
The answer is: No, you are not right. I am a native speaker and would never say "killed the" and not pronouce the "-ed". To be sure, "killed" is not prounounced with two syllables, like "kill-ed", but neither is the "d" silent. The "e" is silent, however. The pronunciation goes like this: "killd".
When I reflect upon it, I don't know why the "ed" is silent. With many verbs ending in "-ed" the "e" IS pronounced. Some examples:
Examples where the "e" is silent and the final "d" is not:
I am sure a linguist could come up with a general rule, but I'm not one of those, so I must defer to an expert. It does seem like verbs whose base ends in "d" or "t" will have pronounced "e" in their "-ed"s.