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Should I try to prevent such situations, say by reraising flop and making him fold (obviously sacrificing my chip EV in the process)? Is it more or less profitable over lots of tourneys?
Also, I do realize this is an early stage where the answer is "yes you were correct". Does this change for later stages?
$EV differs most from chipEV when you are close to the bubble or when payjumps are significant compared to the buyin, which is usually at the FT. The difference between $EV and chipEV also fluctuates based on payout structure and the # players left. For instance, that difference is much bigger when you are 9th/10, compared to when you are 900th/1000 in the same tournament, even though the ratio is the same. Your stacksize and the stacksizes of others will affect your $EV a lot when 9th/10, whilst they have virtually no effect when 900th (assuming you are not near the bubble).
Btw: In the cases where there IS a significant difference between $EV and chipEV, you should be avoiding higher variance (ie. marginally +chipEV spots), rather than bad beats. In the example hand you seem to want to avoid bad beats by playing a high +chipEV spot in a non-optimal way. This is just bad play imo and might even increase variance overall.
A better way to reduce variance in this hand would be to fold the A9o pre, since it is at best a marginally profitable call. Again, this would apply more and more the closer you get to the bubble or a payjump.