Aren't players going to be able to use their league ratings to manipulate their PDGA rating?

Not really. PDGA Ratings are calculated using what's called a zero sum process. The total ratings points earned in a round by the group of players with established ratings (who generate the ratings) will always total the same as the total of their player ratings going into the event.

Let's say a player thinks they can boost their rating in league because they play a course very well. However, many other local league players also play this course well. So even though this player may average 2 throws better on this course, enough other league players also play well enough such that the ratings produced will not average any better from those better scores.

If a player tries to use league rounds to tank their rating, there are already statistical calculations in place to trap that behavior if the TD doesn't already see it and report the problem. Multiple DNF rounds will also be tracked the same way they are tracked for regular PDGA events to discover any pattern of abuse for potential disciplinary action.