No decently designed amplifier should suffer any adverse issues from replacing stock tubes with different brands as long as they are the same type of tube. If you have a 12AX7 in a circuit, replace it with a 12AX7. The amp will be in no danger of malfunction (unless the tube itself is defective). McIntosh should certainly qualify as a competently designed amp.
Now, whether or not you like the sound quality better or not, or whether you have the same opinion as to whether the original tubes selected by McIntosh represent the best sound the amp can deliver, are wild cards. It's your amp so you're free to use the tubes you prefer.

