Pup - thistle control will depend on the type of thistle you have. I have bull thistle, an annual that is easily controlled by roundup in the hedge rows and mowing in the fields (just don' t let it go to seed). I have a neighbor who lets it go to seed, so I keep an eye out for it wherever it pops up.
Canada thistle is a perennial that need a lot more effort and persistence to control. I did kill off a clover field ~5 years ago in a successful effort to eliminate the Canada thistle in it. Unfortunately, the thistle had escaped to nearby afalfa and chicory fields. There I' ve spot sprayed in an effort to minimize crop damage, but have just about given up - I find patches every year. I tried Plateau a few years in the chicory field, but all it did was supress the thistle. This fall, I replanted the alfalfa field in winter wheat after burning the field down 3x' s with roundup. I hit the Canada thistle with roundup in the chicory field whenever the plants got near the bloom stage, and may yet re-plant it next year. I think you too will have to cut down the trees to save the forest (kill off the clover field). I dug out a few websites on Canada thistle fyi:
chemical control: http://www.neweed.org/weeds/weeds.html
organic control: http://www.truehealth.org/acanthis.html

-fsh