There's no such thing as cheating in an unbalanced, alpha-stage, sandbox game.
Well, unless you do something like give your dwarves three pairs of arms, wings, and firebreath...
But simple things like popcap changes are merely adjusting the game more to your liking. Not everyone likes playing the same way- that's why we already have so much choice over things. Toady knows this, and it's why we can now set sooooo many parameters during world creation. It's why we can opt for graphics packs if we can't handle ASCII. It's why most 'regular' games come with Easy/Medium/Hard settings. These things aren't cheats, and the options would not be IN the ini file, fully labelled with descriptions, if Toady didn't want them to be modified.
I played my first few games of DF without any ini changes. I learned the basics of play, got a feel for the game, got a feel for what I liked and didn't like. And then I went in and changed what I didn't like, and gave the game a new lease of life for myself. There's no 'balancing' yet in this early stage, so it's up to us to balance it as we feel comfortable. I usually do minor things like 'show all history' (so I can see full details of engravings), 'show flow amount' (I like to see water depth), popcaps, graphics pack, and disabling sound/intro. One more thing I've done in my current game is to make Unicorns tameable (Exotic, mind you, so I still need a Dungeon Master to tame them). This has made my Mirthful Forest location
ten times more interesting to play as I dot cage traps all over the countryside in the hopes of catching a pair of the beasts and creating a Unicorn Farm.
But none of that is cheating, and truely doesn't feel as such to me. I'd only feel cheating if I gave myself the option to bring Unicorns with me at the embark screen for 1 point each.