In Mahayana, the key distinction is sentient beings vs non-sentient beings. So plants and bacteria would be non-sentient beings and there would not be a violation of the first precept. And eating bacteria wouldn't be a violation of the 3rd minor precept. I'd note that in the linked translation, the 1st precept also is qualified by "sentient beings".
It is also worth nothing that Buddhism is not a homogeneous thing with homogeneous followers, so over time people and Buddhists have learned more about science and had to react to it. Sometimes this means ancient science got incorporated into the religion, such as beliefs/theories about the biological mechanisms of reproduction, or theories about circulation in the body. As a modern Buddhist, I'd dispense with the ancient, incorrect science and think about what ancient Buddhist would have said about biology if they were better informed with modern science. (And I'm not talking about science vs religion here, I'm talking about, what if ancient thinkers knew about bacteria and the cognitive capacities of bacteria) I think they would deem bacteria insentient and incapable of suffering.
I don't know why the lady at the temple didn't like the question. If it was a Mahayana temple, reasonable chance they felt they were being mocked for following a silly rule. The person asking the question was a half step away from asking "To what extremes would you go to practice your silly religion?" or another common subtext when the topic is nitpicky rules "Gee, you must think you're so much better than us people who use anti-bacterial soap"
If this was a Shin temple, strict following precepts is a waste of time, only faith in the power of Amida will show results. In that case, the lady was just annoyed that the guy did the equivalent of going to a Christian Church and asking what Christians have against eating pork and why Christians wear
Burkas and why they worship cows.
UPDATE. This is an American/Vietnamese temple, which appears to be a mix of immigrant and non-immigrant Buddhism, crossing Zen, Vajrayana, Mahayana, but mostly Mahayana. In this context, bringing up bacterial soap means you want to either agree with someone about vegetarianism or fight with them about it. So if you aren't confrontational, you don't fight with them about it. The stats on vegetarianism among American Buddhists is dodgy, but is ballpark of ~25% which is ten times higher than the general population (give me a specific sect and that can be adjusted higher or down to nearly 0-- non-Japanese East Asian Buddhism is pro-vegetarian, the rest are anti-vegetarian). By the way, if this whole question is about vegetarianism, refer to the pre-existing questions & answers.
Speaking of pre-existing answers, this question about the status of bacteria has been asked before.