The best strategy for containing good deep throwers depends in part on the type of handler position they are playing. If the thrower is frequently in a dump reset position, the number one priority must be that he does not get the disc moving up field. A good thrower with momentum and a trailing mark is deadly. You will often find a defender guard this player well for the first two or three resets and then the defender will get impatient. They'll start to overplay the dump in an effort to get the block and will get beat upline or they'll get lazy with body position and fail to take away the upline cut with their body. The number one priority for defending a dangerous deep thrower lined up near or behind the disc is that they must catch the disc with their momentum moving away from the attacking endzone.
If the thrower is playing upfield, I would try to have our defender play more honest D if they were beaten consistently in the first half. To make the thrower's life more difficult, I would instruct our dump defenders to "sponge" or poach the dumps when the dangerous thrower has the disc. Basically, for the first two seconds the thrower has the disc, the dump defenders should jump into the throwing lane. Again, this strategy is designed to disrupt the rhythm of the thrower and prevent the easy momentum huck. It is also designed to get the disc out of the most dangerous player's hands and to see if the team's other throwers can beat us in a pressure situation.
As for they type of defender, I would first try putting my team's best marker on the thrower. By best marker, I mean the player who is always active on the mark and best understands what the hucker wants to throw. The best way for a marker to limit the damage from a hucker is to make the hucker uncomfortable at release. This can mean making the hucker take an extra pivot, causing him to extend an extra couple inches beyond the normal release point, causing the release to be rushed, or the follow through to be shortened. Good huckers have favorite release points and normal rhythms of throwing where they are most dangerous. Disrupt these by taking huckers out of their comfort zones and you greatly increase the odds of your defender having a shot at blocking the huck. In the end, with a good thrower, all you can really ask your defense to do is to increase the odds of a throw that isn't perfect and can be D'ed.
I would try the revised strategy for the first three to four D points of the second half and make their thrower adjust to the different defensive look. If it doesn't work, I'd likely go back to the force the thrower deep strategy at that point and shift one of my top receiver defenders to covering him.