I would never recommend someone not following their doctor's orders.
With that being said, you may consider talking to your doctor more in depth. If you have never had bleeding or clotting problems before, 6 weeks seems like a really long time. I had the same procedure and method you did. My injection days were Thursdays. My surgery was also on Thursday. She did not want me to inject the day of my surgery, and did have me inject the week before as usual. So I was 7 days out from my shot at the time of surgery. She only recommended that I wait until Saturday to take my next shot (so 2 days after surgery).
Some surgeries, and some doctors, do require longer wait times. But if you are uncomfortable with the advice you were given, you should talk to your surgeon or your other doctor to come up with a plan you are comfortable with.