Reason 1: There is mutation protection in nature- in fact, almost all mutations in nature cause a mutation in relatively unimportant genes that lead to, for example, formation of an extra limb, as opposed to missing important metabolism pathways.
I assume that this is the main reason, because you put it first. What can I tell you - it's just wrong. There is no mutation protection in nature, at least not in the way you are picturing it. DNA polymerase has no idea what DNA it is copying - it makes mutations everywhere with equal probability. If effect of the mutation happens to be very severe, then the organism just dies (maybe even at embryonic stage) and we don't see it. In this sense, DB already has mutation protection, as most of mutations that you see in evo-sims are mild mutations, not drastically crippling the bot.
Also, IMO, DB should always provide flexibility and features over simplicity and instant entertainment. DB has a very specific niche in games, mainly for people already familiar with CS or Biology.
I'm all for features, but at some point it just becomes a mess. In fact, it's already a causing a mess in IM - when I ran my sim in IM mode most of the bots that came in from internet died almost immediately, because conditions in different sims are so drastically different. What I'm saying is that there is a fine balance between usability and functionality. Saying "just add a tick-mark" does not automatically solve things.
cond, start stop etc all can be created through mutations and they can be moved around and deleted by mutations, so these are not meta-commands.