*measures his epeen* mmm still a bit small for this conversation but since I do have some exerience with stun alphas...
You press q and start one or two fast perks before your stun then finish your alpha and AS. Most people don't start healing themselves until they see their hp drop, and lag/server sync and player reaction time is your friend here. Doing your stun first in a stun alpha is a waste of 1-2 seconds of stun imo. I don't have CS on my agent yet so I haven't found the best timing for agents yet, but I imagine it still works.
Another thing you have on your side is when people heal themselves they often just assume it works. Often they don't start spamming heal unless they know they are stunned or suspect they might be about to be stunned. I've noticed that tl5 agent stun ganks usually incite panic and irrational thought (being a victim myself), the advantage is yours. Just figure out the right timing.