Let the script create a file in /tmp then you know as which users the script runs
If the problem is the .ssh dir, would it be possible to create .ssh/known_hosts as a link to /dev/null? That would keep ssh happy writing to it (hopefully) and reading would always show an empty file
To simulate the problem. make an write-protected empty .ssh in your home dir and execute the script. Same error message means you have found the problem
If not, in many cases like this different environment variables are the culprit
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