Given the two choices you provided us with above, then yes, the second scenario is the best of the two, but below is what I would do, if I were you to make things optimal.
Here is the optimal situation in order to get the most from your cardio.
Pre-cardio meal -
Whey protein shake (with added supps if you take any)
DO CARDIO
Post-cardio meal - Whey
protein shake (with added supps if you take any)
That is the ideal nutrition situation for both pre and post cardio...this will create a stable environment both before, during and after your intense cardio sessions.
How is having a whey protein shake before and/or after your cardio sessions going to throw your whole diet out of whack? If anything, it will improve your results, and make the most of what you just did, as well as keep your system in an anabolic environment while at the same time replenishing your nutrient stores from the intense cardio you just performed.
Just a side note: Pre and post nutrition/supplementation is just as important when doing cardio as it is when doing weights. 