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I figured I'd time the difference before we change the code:
$ ./python.exe -m timeit -s 'import rational; r=rational.Rational(3, 1)'
'r.numerator'
1000000 loops, best of 3: 0.696 usec per loop
$ ./python.exe -m timeit -s 'import rational; r=rational.Rational(3, 1)'
'r._numerator'
10000000 loops, best of 3: 0.155 usec per loop
$ ./python.exe -m timeit -s '(3).numerator'
10000000 loops, best of 3: 0.0324 usec per loop
$ ./python.exe -m timeit -s '(3L).numerator'
10000000 loops, best of 3: 0.0356 usec per loop
$ ./python.exe -m timeit -s 'from rational import Rational' 'Rational(3,
1)' 
10000 loops, best of 3: 80.4 usec per loop
$ ./python.exe -m timeit -s 'from rational import Rational;
r=Rational(3, 1)' 'isinstance(r, Rational)'
100000 loops, best of 3: 10.6 usec per loop
So every time we change .numerator to ._numerator we save half a
microsecond. If we construct a new Rational from the result, that's
totally drowned out by the Rational() call. Even checking whether we're
looking at a Rational costs 20 times as much as the difference, although
that can probably be optimized. I think this means that we shouldn't
bother changing the arithmetic methods since it makes the code more
complicated, but changing unary methods, especially ones that don't
return Rationals, can't hurt.