After Christians took control, it became standard in the Roman empire for Christians to take over pagan temples and transform them into Christian churches or basilicas. The same was true of course at Baalbek. Christian leaders Constatine and Theodosius I built basilicas on the site -- with Theodosius' constructed right in the main court of the Temple of Jupiter, utilizing stone blocks taken from the temple structure itself.
Why did they build basilicas in the main court instead of simply rededicating the temple itself as a church? That is, after all, what they did with the Pantheon in Rome and it certainly has the advantage of saving time because you don't have to build something new. There are two reasons why they would do this, both connected to important differences between Roman and Christian religions.
In Christianity, all of the religious services take place inside the church. In Roman religion, however, public religious services take place outside. This main court in front of the temple is where the public worship would have taken place; in the above image, we can still see the base of the main platform. A large, tall platform would have been necessary for everyone to see the sacrifice. The cella or inner sanctum of a Roman temple housed the god or goddess and was never designed to hold large numbers of people. Priests performed certain religious services in there, but even the largest weren't designed to host a crowd of worshippers.
So to answer the question about why Christian leaders would build churches outside of a Roman temple instead of rededicating the temple itself: first, placing a Christian church on spot of pagan sacrifices carried a lot of religious and political punch; second, there just wasn't room inside most temples to house a decent church.
You'll notice, though, that the Christian basilica isn't there anymore. Today there may only be six columns left from the Temple of Jupiter, but nothing is left of Theodosius' church.
