I wouldn't pick Flintoff without an injury to the main 4. Still doesn't have enough overs under his belt this season. I know it's been suggested he doesn't have to lead the attack but this attack needs a leader. If Sidebottom is out, pick Jones or drop Broad for Jones, whatever.
But, either way, picking Flintoff and then bowling him less because you're worried about him being injured is a low-percentage move; you can't and shouldn't protect guys at Test level because even at his best, it's not as if Flintoff was a fast bowling genius (a la Marshall, McGrath, etc.) who you simply cannot do without and even half-fit will run through Test sides. At his best, he's a dependable, attacking wicket-taker and he'd definitely not be at his best right now. If there are any doubts about him being able to bowl long Test spells, you simply should not pick him.
If and when he can bowl the number of overs expected of a Test bowler, get him in because he's probably still one of England's best bowlers.