If it's the flippy disk, don't you only have to copy side 2? Side 2 shouldn't be copy protected (normal DOS diskcopy should work.) Then you just boot on side one of the original disk, then after the opening sequence is over, put in the copy of side 2. Not the optimal solution maybe, but would get you playing without altering the original.

If you decide to go with the Kryoflux, you will need to tell it "not" to read side 2 of the disk, and then physically flip the disk to read side 2 with the Kryoflux. A PC flippy disk should have 2 index holes (one for each side.) So you can do this with an un-altered 5.25" drive. Though, if you have the funds, and plan on ever collecting other format flippy disks (C64, Apple II, Atari, etc...) investing in a modified 5.25" drive would be a good idea.