As I see it there are two strategies that Evernote might pursue if it doesn't want this automatic strikethrough "feature" to drive customers away. The first and most desirable would be to make the "feature" optional. Failing that, it should provide a decent workaround.
The checkbox workaround is ineffective because a <CR> at the end of a line beginning with a checkbox converts that and subsequent lines to the checklist format (with mandatory strikethrough). I thought I could defeat this problem by preceding each checkbox with a space, as suggested above. That seemed to work during my original creation of the note, but when I returned to it the next day the first <CR> I entered converted the entire note to the new Checklist format.
Another workaround that should work, but does not, would be manual removal of strikethrough formatting. This should be possible in two quick and easy steps: (1) select the text to be un-struck, and (2) click the strikethrough symbol. To un-strike the whole note, one would (1) type CTRL-a to select all text; (2) click the strikethrough symbol to give that format to the entire note; (3) with the whole document still selected, click the strikethrough symbol again. This should remove all strikethrough formatting in the document. But because the mandatory strikethrough formatting in the new Checklist format cannot be manually removed, none of these steps have the desired effect.