I used to worry about the purple goo, but I don't worry about any longer. Here's what I do now:
1. Figure out the maximum number of items I can crucible in one batch. For Thaumium, for instance, I think it's somewhere between 4 and 6 Thaumium ingots in one batch when using mossy cobblestone as the source of Praecantatio. It's messy, but cheap.
2. Dump in all ingredients for the Essentia (ex. 24 mossy cobblestone to target 6 Thaumium ingots in 1 batch)
3. Dump in the matching number of catalysts to match (ex. 6 iron ingots to make 6 Thaumium Ingots)
4. Use wand to purge
5. Ignore goo and repeat for next batch
Only at the end will I bother cleaning up the goo. I have my Crucible indoors and only once have I had a taint blob spawn during a session where I made a stack of 64 Thaumium ingots before cleaning up, but it was all good 'cause I needed the Vitium anyways.
*Note : It's often more efficient to make 2 or even 3 batches before purging. In the above example using mossy cobblestone to make Thaumium ingots, it's actually more efficient to make 2 batches of 4 Thaumium ingots, and then purge. 4 Thaumium ingots requires 16 mossy and 4 iron, which are natural splits of a stack of 64. Quick and easy.