In some episodes she is, in other ones she is eating (or trying to eat) a turkey sandwich or cooking dinner (chicken). I am confused and would like to know if this is the problem of many writers on same TV show?
She wasn't a vegetarian when the show began. However, to quote from the wiki:
So, after Season 1 she became a vegetarian. This would also suit Emily Deschanel, who is a vegan.
However, despite being a vegetarian, it doesn't mean she won't cook meat for other people (many vegetarians do).