Check your client settings (Tools > Options > New Documents > Settings) to see if you have "Generate Laserfiche pages" or "Generate searchable text" checked, or if you checked either of those in the initial import window.
Either of those options will require access to the document content, which means the password is required, but if neither are checked, it should just import the PDF without trying to open/access it.
The same would apply to the Save to Repository task if the connection profile used in Forms has either of those options enabled (generate searchable text might be enabled by default).
You can log into the client with the account used in the Save to Repository profile, and from there you can disable settings like that.
However, doing so would only prevent the save error and wouldn't resolve the overall issue, which is why I suggest the workflow approach.
That approach can detect inaccessible PDF files upfront so you could just reject the form outright and send a message back to the submitter letting them know one of their files was either password protected or corrupt.