The ending made sense. The whole time, they killed people who stood in their way to accomplish their (selfish) objectives. What happened to Togame is no different, her existance was in the way of the princess who was trying to correct history, just like Maniwa corps and the current shogun.
Right before the final "cherio", Shichika asked the princess if she hated Togame. At this point, he was simply confirming that her action werent based on hatred, but it was a duty she had to accomplish. Her answer, mixed with the fact she was ready to die to complete her objective, confirm she wasn't a bad person..or at least, no more than Togame.
The only part that piss me off is that they had to spell it out clearly for you during the credit. They didn't need to make the princess look like Togame to get the point accross..it was fairly obvious from the scenes before. Seeing her follow shichika doesn't bother me (and make sense), it's just how she is acting that is out of character.
In the end, the only thing I'm not entirely sure is Togame's motive. I would put my money on it being a lie (or at least, partial lie), but it could be understood either way. I don't think it's really important since we already know she wasnt a bad person, it would just make her death scene better if it was a lie.
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And I was kinda hoping he would go back with the dojo chick, but w/e works.