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If you are doing serious stuff with Moodle, then you should have at least two completely separate installs anyway. That is, you should be able to make a copy of your live system at any time, so you can test upgrades, and new plugins, on the copy, before you risk upgrading your live site.
So, it should not be a difficult thing to run two completely separate live sites, if you have good reasons to keep them separate, and it seems like you do.
However, for ease of maintenance, you may decide that the two sites should use exactly the same code. That is, you install exactly the same plugins into each site, and upgrade them at the same time.
So, it should not be a difficult thing to run two completely separate live sites, if you have good reasons to keep them separate, and it seems like you do.
However, for ease of maintenance, you may decide that the two sites should use exactly the same code. That is, you install exactly the same plugins into each site, and upgrade them at the same time.