Ignoring the threats of infection from xeno micro-pathogens is really just one of those suspension-of-disbelief things that we're asked to buy into so the story doesn't get bogged down with dreary scientific exposition when the writer/director just wants to get on with the real story stuff i.e. the drama.
As sci-fi fans we're used to this kind of thing: Faster-Than-Light travel, and lack of relativistic effects therein, FTL interstellar communication, artificial gravity etc etc. I'm pretty forgiving about these issues, so long as the rules are established early on and then honoured by the writer. But that's where Covenant broke the rules. When the landing party opens the door and marches out into the open air, what I was being told was that in this story universe micro-pathogens don't exist. (OK, I'll accept that). But then the plot tells me, hang on, lethal micro-pathogens do exist - ha ha fooled ya!
Now I have to rationalize this somehow. The obvious answer - these characters are stupid, the protocols they were trained with were stupid, the general IQ of humanity (and its scientists who devised the protocols) has descended to moron level.
At this stage, I'm having great difficulty buying into the level of suspension-of-disbelief necessary to take the story seriously.
I can excuse most other flaws in the movie, but when you betray this suspension-of-disbelief pact you have with your audience (albeit an unwritten one), that's unforgivable really.
TC