Clock input

No. The more things you route through, the more jitter can get on the line. The clock pin is special because it routes directly to the PLL. If you come in on another pin, it has to route to the PLL. From a physical perspective, there is no way to get around this.

Be careful about reading too much into this warning. It's telling you that it could be better, which is nice if you haven't laid out your board. It's not telling you that you will have horrible jitter. What's your requirement? What are you measuring as the output jitter? Are you getting failures? (My guess is your current setup is fine, but I don't know without understanding your requirements.)