How can I keep ghosts out of my machine?

You don't have to obstruct every area in your enclosed redstone circuits. You can easily place normal torches and/or Glowstone blocks throughout the enclosure. This will also aid in visibility within your ICs. Redstone can be placed on glowstone blocks, but they exhibit interesting properties, so be careful

Redstone can be put on glowstone, but being a transparent block signals can pass from one block to diagonally another with glowstone "blocking but not blocking" it, making possible nearly instant vertical redstone and new vertical logic gate designs.

I suggest torches. Keep your circuitry well lit.

Well, Why use obsidian? It's just a pain to remove and no more protective from mob spawning than say, cobble or dirt... Also you could have an actual room lit with torches for your circuit instead of fully enclosing it in a shell.