I don't use your plugin, but have at various times thought about using it (and have tried it out a couple times), so take that into account when reading my opinion.
I think that if you include the stats while these conditions exist, you should branch your plugin into 2. One as it is now. One with the stats. Provide the first one as it is now, through calibre, and provide the 2nd one as a beta (and not in calibre's list of plugins), much as davidfor did when he first was developping KoboUtilities. Then the people who don't go to any bother figuring out the implications are much less likely to get their hands on the more problematic plugin and cause a lot of headache with their complaints of things you have so logically laid out in the OP.
I think it's also important to note, that there are probably people who like the plugin as it is, even without the stats for other features that it can provide (layout, footnotes, etc). And there may be people who don't want the risks or problems associated. This would ensure both camps are happy and getting the most out of your plugin.
Now, I realise updating 2 plugins with potentially very different code could be a dealbreaker for my idea. I don't write code and don't in any way think you are obligated to do any more than you want and feel is a good use of your time. So feel free to dismiss this idea altogether. If the existing plugin could stay basically as is (don't know how much you have to change each kobo fw update), and you could branch out and put most of your time in the new plugin, that might be a workable solution as well.
Thanks for the heads-up about what this change would entail as I have been following the progress with a lot of interest.
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