I wouldn't worry too much about Witch Hunters.
Yes the points you outlined are their strengths, but they are strengths that you can in part negate with your Ork Force.
For example if you have a heavily transported force say a backbone of 3 squads of 20 Slugga Boyz in a a Battlewagon, you negate most of the hazard that the Flamers present as the Battlewagon protects them, and with the Battlewagons you can outmaneuver and block charges to your infantry by the Penitent Engines.
There are a few things I would advice against the Sisters of Battle like the SAG Mek, which on a double 6 can and will remove some Sisters with no saves allowed or to Wound rolls. Even if you don't get the double six, the SAG can and usually does cause a large amount of carnage before its taken out by the enemy or blows himself up.
A unit of 3 Kannons would help tremendously as well. Three Str 8 Shots into a unit of Penitents at the Best BS the Ork army can throw at them, plus the ability to re-roll 3 misses in the whole game, AND how they can be used for some quick blast template pain against the Sisters (oh and how you could also re-roll that scatter) makes them very potent and cheap anti-Witchhunter weapons. Oh I almost forgot to mention, they usually aren't a high target priority for your opponents as most are more concerned with shooting up a green tide rather than their artillery.
Last but not least I'd recommend Stormboyz. They're fast jetpack goodness can outstrip the speed of the Seraphim and can earn you the charge against many of the SoB, which will make the decisive difference in your casualties. More than other opponents you need to get the charge on Witchhunters, otherwise your on your way to a burning death.
As for the Faith Points, yes it can seem a little overpowered (maybe more than a little), but hey them's be the breaks. Every race, especially in the codex's produced at that time had (many still have) strange overpowered rules, like the Necron's WBB, or the oldschool Orks 'Mob Up' rule or any of the Craftworld rules for Eldar players.
Its nothing to be too concerned about, on paper it may seem kinda scary, but its not as bad as it seems.
Peace
~OD