Make a custom 404 that resembles your homepage with no follow meta. There isn't any good solution if your site is down - period. If it's your hosts fault - move your hosting. If it's the scripts fault - change scripts. If it's user error running the script - stop doing that ;)
I'd leave it. Google's used to seeing sites suffering code errors on visits. It's less use to robot instructions which change all the time. Google may only look at robots.txt every week or so and meta instructions a little more often.