I think I see the problem. There is no way autoroute will avoid those other traces, as what you got is what most people want.
Some options to avoid that:
1) Only allow autorouting on one side (say bottom). That will be very ugly.
2) Do not use autorouting.
3) Use autorouting and rip-up the traces that cross the pour. Then manually route just those traces and any others that need to be changed.
4) Don't use a polygon pour. You can define that area as a "do not go" place. Autoroute, then manually add your high current trace.
5) You might try reversing the order in #4. That is, manually route the one wide trace. Then autoroute, if your version allows that.
Your version of Eagle may have additional controls. If you can't select just one side, then make the cost for the top or vias very high. If that improves things, then manually route those signals that go into the pour.
I have never used autorouting (Eagle ver. 7.2 or 7.7) for a final design. What I will do sometimes is use autorouting to help improve parts placement (where such placement is not dictated by other factors), or get some ideas. I then ripup and route manually.