Nah, you have nothing to worry about -- your tomatoes won't be pungent with any suggestion of manure.
Incidentally, I've just tasted my 2nd round of Black Krim tomatoes and the taste was richer than the 1st time. Definitely a gentle smoky essence to them, VERY delicious and no salt required! I'm eager to see if this is more the norm for the tomatoes produced from these plants. If so, I'm growing Black Krim again next year.