I have posted on this topic before, but maybe I will add something I haven't yet covered.
1. The amount of and dedication to training required to bulk muscles to the point of decreased flexibility is high. The diet and physical regimen of such training is typically specific and severe.
2. The role of physical fitness and isolated muscle exercise is present in almost every athletic endeavor we have, martial or otherwise. I have not yet read anything [medical] that suggests proper exercise is detrimental to physical activity.
I used to joke when my personal trainees would comment about how their 2-3 hourly sessions per week might "bulk them up". The argument as I have heard it best presented relates to the inability to relax muscles or groups while trying to perform aikido. In this context, the argument relies upon the practitioner participating in a extreme training regiment that focuses on muscle building while lacking stretching and conditioning. Of course, the truth is there are more aikido people in poor physical health then there are these hulking monstrosities.
I think also it should be noted that as I look more closely at kata I am starting to find that if I encounter resistance it is because my kata is wrong, not that I am magically turning to stone. While I think we all understand that aikido involves a level of precision akin to surgery, "relax" is not quite the satisfactory answer we are looking for to resolve our shortcomings. I may be using one muscle when I should be using another, but the answer is still not "relax"; it is of course, "stop using muscle X and use muscle Y."
As for Kevin. I did [in] my ACL in when I was 18 - took 8 weeks of rehab and another 4 months to gain back the strength and muscle I lost from the injury. In May, I partially tore my MCL and am now back in the same boat. Good luck.
There's nothing wrong with muscle. There's nothing wrong with a lot of muscle - except maybe in some of the extreme cases talked about above.
The real problem is that the kind of conditioning associated with most conventional weightlifting makes it very hard to do some of the training that's important for internals.
That's really why a lot of folks suggest you lay off one thing while training the other, until you've got enough of a grasp on things that you can work both together.