Bots, I believe, use the cast code located in MobAI.cpp, which controls NPCs too. Specifically, do a find for "NPC::AICastSpell" and I believe that's the function bots/NPCs use to determine spell choice. I did some poking around trying to build a better healer, too.
Edit - I had an idea for a tweak. I noticed in the table for Cleric Bot spells, the HoTs are listed as type 2, a healing spell. Perhaps if they're changed to type 1024, which is for in-combat buffs, they might only refresh HoTs when nobody needs healing? This however might make them keep HoTs going on the entire group which would chew through mana pretty hard I think.
You could also try some custom code in bot.cpp's "Bot_AICheckCloseBeneficialSpells" function, which is what determines the call to AICastSpell, this wouldn't intrude upon NPC spells at least.
The easiest solution is probably to just remove the HoTs from the cleric bot list of spells. GeorgeS's Database Editing Suite works nicely, although there's no confirmation on deleting an entire table (as I found out first hand from an accidental misclick where I deleted the entire Cleric Bot spell list) so do be careful if you use it:
http://www.georgestools.eqemulator.net/
If you have your own database editing software, Cleric bot spells are ID 701 in npc_spells_entries, this query will return all 75:
SELECT * FROM npc_spells_entries WHERE npc_spells_id=701
Then it's a matter of getting the spellid for the HoTs/spells you want to remove and deleting the relevant lines from the table.