You could look at it the other way. When it's deployed as a binary, no one really can be sure what it is doing, without extensive effort. Whereas a conventional script can be easily scanned, to see what it is doing.
If you want some security with a script, just have it's permissions and ownership set, and maybe do some cryptographic fingerprinting of it.
I would be very suspicious of any binary I was asked to run, unless I compiled it myself.
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