I don't know what exactly you're asking, Raspen.
To the OP: Personally I wouldn't antagonize the PCs for using an effective tactic to keep their low-level characters alive, but I would keep them from abusing it overly much.
One thing that might help would be throwing in a low-level evil cleric NPC, who's taken control of a handful of skeletons through Rebuke/Command Undead; the DMG stats may help get this NPC ready. The cleric stays well away and has some tiny skeletons or whatnot standing around him in a defensive perimeter, while sending some medium or small skeletons to attack the party. PCs waste a round or two just getting into melee with the cleric to Intimidate him, and close enough for the other PC to Cause Fear, while the skeletons do some minor damage and totally ignore the fear-mongering.
Meanwhile the cleric is casting Remove Fear on himself (for the morale bonus against fear and Intimidate), having heard or observed before that the PCs use fear as a weapon. Or casting something like Spiritual Weapon, Bless (so his skellies can hit more than just once in a while), or Summon Monster I or II (for some minor fiends to keep the party's casters occupied with flanking beasties). A challenging encounter, but if the skeletons are all weak ones (human, halfling, kobold, or sprite skeletons for instance) and the evil cleric is something like 3rd level, it shouldn't be too tough.
How about replacing or adding in some encounters with 1st-level kobold rogues or something? 1st round, the kobold rogues with Improved Initiative as their feat surprise the party with superior stealth and spotting, charge in and sneak attack every PC for probably 1/2 or 1/3 the PCs' HP (or gang up on two PCs to take them practically right out of the fight before its even begun), 2nd round some kobold or another is likely to win Initiative (even if they don't all somehow win Initiative) and get in another Sneak Attack against a still-flat-footed PC, like the rogue/warlock PC. Suddenly, the PCs have to fight a few meek, but kind of deadly, 1st-level kobold rogues without the benefit of their Big Bad Intimidator. The kobolds could even be using saps for subdual damage, intending to rob the PCs and take them captive for someone else.
To adjust the stats of the standard 1st-level kobold warrior in the Monster Manual, add the following adjustments to the existing stats: -2 HP, +5 initiative, base attack/grapple -1/-1, attack or full attack (-1 to the attack roll modifiers presented there), special attacks Sneak Attack +1d6, saves -3 to Fort and +3 to Ref and +1 to Will, ability scores (change Dex to 14 and Con to 9, and change Int to 9 and Wis to 10, from switching their base scores before racial mods), skills (only important changes are another +3 Listen and Spot, and another +4 Hide and Move Silently), and feats (replace Alertness with Improved Initiative).
Chances are decent that these guys will get the jump on the PCs and disable or nearly disable the fear-mongers, then perhaps some other NPCs from the module could make their presence known and move in to assist the kobolds (if any survive long enough beyond their first 1 or 2 rounds of sneak attacking the bejeezus out of some surprised PCs). Remember that the kobolds will probably charge or partial-charge on their first action, getting +2 on the attack rolls and probably getting surprise (with flat-footed PCs likely losing any Dex bonuses and dodge bonuses to AC).
Goblins could be substituted for kobolds, but the stat differences would be a bit different and goblins have slightly higher CR than the lowly kobolds.
You could instead just throw in an NPC cleric (use stats from the DMG) or two that has Remove Fear prepared in one or more slots, and doesn't get anywhere close to the PCs until after other NPCs have gotten the party's attention. Cause Fear has a range of Close, so unless an NPC cleric starts the battle close to the party (and visible), he or she should be able to move in and Remove Fear for the NPC bruisers. Also note that Remove Fear gives a morale bonus on saves against fear; that +4 could give NPCs a moderate chance of resisting the Intimidate checks, even after suppressing the first fear effect upon them when cast (after they get either Intimidated or Cause Fear'd).