Multiple followers, and moving onto shrines in the Count expansion
1) Yes, you can certainly have multiple followers of different colours in each quarter. This is quite explicit in the rules:


  ...when a city, road, cloister or farm is scored, all players with followers in the appropriate quarter of Carcassonne... may move their followers from Carcassonne to the scoring feature before the majority is determined in the feature being scored, unless the Count is standing in that quarter of Carcassonne.


The ability for each player to store up multiple followers is an essential part of the strategy for the expansion.

2) Yes, shrines are treated as cloisters for the purposes of moving followers from Carcassonne. From the FAQ at Carcassonne Central:


  Can I move followers from the city of Carcassonne (from the cathedral?) into a shrine during scoring?
  
  Yes, shrines and cloisters are treated in the same way.