If you have lots of hiding places and not too many fish in your main tank, I would let the female out. Many of the fry should survive so, unless you want ALL of them, there is no reason to keep the female in there (which is stressful and frustrating).
Most guppies will give birth to about 5-10 fry at their first pregnancy. From then on, healthy fish can produce 50 or more and it increases with size, age and feeding/health. Usualy most will be eaten which may explain why so many people say their fish only give birth to small numbers of fry. Very old guppies will have fewer fry.