Hi Ronen,
The best way we've found is to rely on the web page visit following the email click. For our audience, I haven't been able to identify large pockets of bot web visits in the 'visited web page' activity, but I can tell you that many other Marketo users have see those visits skewed by bots as well.
Something we have done is to change the Set Success program we use to mark members as 'engaged' in the program, and no longer completely rely on the "clicked" metric and instead view the program success percentage.
For our Set Success, we use "visits web page" as the trigger, and since we tag every email URL with google analytics tracking, we use the GA campaign value for that email as a constraint on the trigger to identify web traffic from that specific email. Like this:
You can use a similar batch program to look backwards, saying if someone was on the website with a ga campaign tag for that email and run a list to see how many people actually clicked a specific email, but that's an adhoc way to run numbers email-by-email instead of broadly.
Hope this helps!
Chris
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