Providing bad odds for opponents' draws, but what about their implied?

[PokerAmateur4]

Note: This applies to both MTT and STG but I play more STG so would love to hear about the response from more of a STG perspective if not both.
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I am reading Hoh2(Harrington on Holdem Vol.2), and it has reminded me of a question that I have been mulling over in my head.

This question is what is the right amount to bet an opponent when you are fairly sure you have the best hand after the flop or turn.

Here is an example which he provides:

Major event, final table, 6 players.

BB 1200 SB 600. Ante 200. Pot 3000 to start.

Hero in BB, JKs.

4 Fold to SB who calls.

3600 in pot. BB bets 3600, SB calls.

Pot 10,800. Ac 10h 5h. SB check. BB check.

Qh. SB checks.

Analysis: so at this point you must bet. You would like him to call for something but not allow him to catch a card which provides him a winning straight, full house for free, or a flush.

Harrington suggests a bet of 5,000 here, half the pot, to give the opponent 3-1 odds, where he needs 4-1 for a flush draw. This would then be a benefit for you if he calls, Mr.H implies.

Imagine if the opponent does make a flush on the river. The pot would then be 20,000. Imagine he then bets 6,000.

Assuming he can expect a call from you, and that you must make the river call, I belive his implied odds on your turn play were in fact 21-5, 4-1, even money.

I should have a better example where the river call is more essential and neccesary for Hero and the implied odds of your opponent end up being +EV, I'm sure these exist but I cannot create one easily.

Perhaps the bet Hero can make on the river assuming a miss conteracts the implied odds of Villain making the flush? I.e. the chips Hero makes on the river when the opponent stays with a losing hand allows Hero to leverage a 3-1 bet against opponent?

In conclusion, is Harrington's advice on turn bet size correct, or is it too small? How should one practically consider making bets such as the one Hero must make on the turn in this one.