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Having practiced yoga a bit myself I know where you are coming from with all the benefits that yoga can provide. I do swimming as part of my cardio cycles, it's one of the best cardiovascular exercises around.
However, to be complete it's hard to ignore other training principals such as lifting weights and running.
A good rule of thumb and to keep it simple is to set goals in your martial arts training and then use your exercises sessions to achieve those goals. Example, say your stiff as a board and you can't high kick with your left leg... using yoga-type postures and working on the flexibility of your low back/hamstrings coupled with heavy bag kicking increasing in the degrees you can kick upwards should over time get you to a point where you can head kick. If not, evaluate what is holding you back and then work on that point.
Combat sports is unique and challenging because you have to be well-rounded. You need speed, agility, flexibility, power, strength, iron-will, heart... to reflect those attributes you need to progress on many levels at the same time. By limiting your training choices then your tool box isn't as deep to work with on developing yourself as a complete fighter.
Don't be afraid about injuring yourself lifting and running. Unless you have previous injuries or an aptitude to getting injuries (arthritis in the knees would be a knock against running) then you can safely apply any training principal to whatever goal you have.
Like anything, use trial-and-error. If it's not feeling right or working towards your goal(s) then re-assess and move into something else. Never limit yourself just because you think or someone told you that you should or shouldn't do it... always do it and then evaluate afterwards.
Hope that helps, good luck.
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