Being on holiday at the moment, I'm away from my reference shelves, but even cursory net searches will bring you up great examples. Cordoba Cathedral was a notable example, for instance. Some other examples are given at http://en.wikipedia.org/wiki/Christianised_sites - even though it's Wikipedia, it's reasonably reliable and squares wit my more academic texts although it's far from an exhaustivve list.
The New world itself had many examples (e.g. the complete dismantling of a pyramid to build Museo Nacional de las Intervenciones) and other similar ones. In Europe, the common game was to usurp a holy well or similar site by retaining the holiness but associating it with a christian saint or deity.
It's a traditional game and noone was guiltless - as I have already said however, it is abominable today and to be condemned , whether at the Bamaiyan Buddhas, the BJP mobs in India or now at this Christian/Jewish site in Iran.
You’re both reaching back into very ancient history when you mention Christian temples built on the site of pagan holy places. We could also examine the state of the law and individual rights 1,000 to 5,000 years ago. Most groups of people left those practices behind centuries ago, with the notable exception of the Moslems who’ve also desecrated Jewish holy sites around Jerusalem in recent years.
Some also love to cite the Spanish Inquisition and use that to take some of the condemnation off contemporary sharia law and veiled women and honor killings and death for apostates.
When is the most recent example of Christian churches being built over some other faith’s holy site? The most recent site for Islam seems to be this week.
Citing Christian practices from many centuries back as equivalent to Moslem practices this week is pretty weak. One group seems to have continued those practices.