Too much cardio burns muscle? Really? A properly fueled and rested muscle will be broken down by the body at what point? Is it after 20 minutes? After 23.7 minutes. 34 minutes, but only on Thursdays?
What about a muscle that isn't properly fueled and rested? Will it be broken down sooner? How much sooner?
Basically what it comes down to is that the body is an amazing machine and will respond to outside stimulation the way it has been programmed to since birth. You are not going to reprogram your body. That is impossible. What you can do is work WITH your body instead of AGAINST it to accomplish your goals in a way that is healthy and stress free.
Since your cardio is geared for stamina and not fat burning, don't feel bad about hitting some carbs prior to beginning. Don't do intense cardio post work out or first thing in the morning as stamina and endurance training will require a longer period and duration to have maximum effect. First thing in the morning and post workout is when your body is basically running on empty (in morning) and in a state of recovery (post training). The aminos, glucose, etc... in your body will be out of whack following training or an 8 hour fasting period. This is ideal for losing weight with short intense sessions that force the body to break down fat for energy. But at longer sessions it becomes counter productive.
Try incorporating your cardio on an EOD basis with no weight training at all that day. Maybe calves, abs, and stretching prior. Follow a generic drill format. 1 minute being an intense whirlwind followed by 5 minutes being a breeze, 1 minute rest. Back to 1 minute whirlwind, 5 minutes breeze. Repeat this cycle 4-5 times. After a couple of weeks, try to do it in the same way 1 minute whirlwind but this time only 3 minutes breeze. That way the intense sessions come more quickly. When you can do it 4-5 times in a cycle only resting that 1 minute in between cycles, then increase it up some, but in the same format. This time it would be 2 minutes whirlwind 5 minutes breeze 1 minute rest. Few weeks of this, adjust it like before. 2 minutes whirlwind, 3 minutes breeze, 1 minute rest.
Afterwards make sure you feed your body with BCAAs, fast acting carbs, and solid nutrients from clean food within 45 minutes.