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It could be possible with some code changes but I have found that it can also cause more trouble than it is worth. It is far better to just put my plugin on all your sites and make special considerations for those sites that are not WordPress.
Just to give you an idea of the problems you may run into when scanning many sites at once, here is a short list of just some of the most common issues:
1. PHP has a very small memory_limit so the scan process many not be able to index all the files on so many sites all at once.
2. Even if it is able to build the initial index and start the scan it will likely still take a great amount of time to scan many sites in a linear way, as opposed to installing multiple copies on each site and running multiple scans at the same time.
3. Timeout and lag-time in large scans can cause scan errors that will make the scan process restart some steps and that could take even longer and render less accurate results.
4. Some directories above the site root are protected or may have different permissions which can also cause read errors and this will bog down the scan even more.
5. If there are any sites that are not WordPress then there is a much greater chance of False Positives, which could lead to incorrect modifications in proprietary code that is not malicious, and then could cause site errors.
6. Some browsers may even crash or lockup before the scan is complete due to the sheer volume of data returned by the scan that the browser has to process.
These are the main issues that I am familiar with and could recite off the top of my head but I know there are more reasons to avoid combining all the sites into one scan. I know it is an attractive idea to have all your sites scanned at once, but trust me when I say, it is just not practical to expect a PHP page running inside a WordPress plugin to handle that much work efficiently or accurately. There are command-line tools and server-side anti-virus programs that can scan all your folders, they are just not as good as my plugin at identifying and removing malicious code from WordPress files.
