The commissioner of the RCMP, of course, is very concerned about making sure that any evidence he presents can be used in court and won't be thrown out for whatever reason—principally that there's a violation of the charter or that it was not obtained properly, etc.
On the other hand, of course, you have the principle of Parliament. Parliament is supreme and can look into things if it wants to.
What I think he's pointing out in this letter is that what the committee has asked for could potentially cause problems down the line. He wants to, in effect, alert you to it.
He's quite right. These are two difficult principles to reconcile. They can be reconciled, but you have to be very careful. He wants to make sure that nothing impeaches his duties as independent law enforcement. On the other hand, of course, he's very careful in not wanting to tread upon your privilege as a parliamentary committee to ask for whatever you want. If both parties are aware of the problem and act carefully, these actions can be reconciled.