Why did congress pass laws that restricted the influence of the lds church in the territory?

There were a couple of reasons:

1) At the time Brigham Young was the President of the Church and the Territorial Governor at the same time. This made people back East very nervous, manly because the were worried that he would set up a little theocratic kingdom and mess up their plans for a US that stretched from coast to coast.

2) The South was prepping for the Civil War, and needed a distraction, so they claimed that the Mormons were in rebellion out west. President Buchanan then sent out an army to put down the rebellion and install a new governor. Long story short, there was no rebellion, a good chunk of the army was occupied out west during the first couple of months of the civil war, and the Utah Territory got a new governor anyway.

3) It was profitable. When Congress outlawed polygamy one of the punishments they used was seizure of property. The vast majority of Church land (chapels and etc) were seized immediately and the Church ended up heavily in debt from having to buy back the land and buildings that they had settled and built originally.