The problem is that Thermalillies are either impossible to automate, or blindingly easy to automate depending upon your set of mods. Which make them either just this side of powerless or just about the only thing you'll ever need.
I can't think of a way to nerf them in packs with Blood Magic, Thaumcraft, Buildcraft, or BluePower without outright nerfing them into unusability in a pack without liquid placers and or lava producers. Other than a greedy consumption mechanic. Which requires little effort to implement and doesn't change how it functions in a meaningful way beyond requiring timing.
Maybe a radius diminishing return multiplier? I guess you could make it able to eat lava from a really wide radius but work a lot like the MFR sewers in that overlap in areas causes a malfunction? That would make them useful for eating lava lakes, and then you could transfer the mana with warp lenses and/or mana storage devices like tablets.
Actually... that's something that might be useful. Something that can detect if a flower/altar/brewery/etc is currently storing mana from a short (8 blocks?) distance and emit a redstone signal. It would allow people to more easily automate the delicate timing based flowers without relying on honestly flaky MC timing methods. Make it Elven Knowledge and require beating the Gaia Guardian but make a few at a time per spirit. Then the "problem child" flowers aren't immediately the One True Setup because of power/skill ratio, but when you progress into the endgame of the mod you can MAKE them into the One True Setup again assuming you don't want to deal with the hassle of one of the more interesting builds.