I think it depends on the kind of meditation you are doing. If you are doing a meditation aimed at developing a particular state, such as compassion, then you want to control thoughts to bring everything to the state of compassion. If you are doing intense concentration on the breath, you want to control thoughts so they do not distract from the concentration on the breath.

However if you are doing awareness (mindfulness, Zen, etc) meditation, where you are simply watching the contents of mind, then you can let the thoughts rip. You watch them come and go and the aim is to maintain awareness in the midst of all the ripping thoughts.