One thing about reptile metabolism, you generally have time to act before it's too late...
We really could use more information about exactly what size food item and frequency your snake has been eating, if it's gone off feed, whether it's behavior has changed suddenly or if it's just the skinniness you're worried about.
Please tell us also about the size and furnishings of enclosure, and if you have any supplemental heat or track the humidity levels. Also if you ever use calcium dust or water additives, that can be important or not depending on the food items...
Snakes often defecate in thier water and ingest some amount of it, their guts function a little differently than mammals, so if it helps to answer your question directly- no, it probably wouldn't have hurt your snake to drink a little dirty water for a couple days...you got an unsolicited earful because we all so often see a snake in a petshop or home that is neglected with a foul water bowl and dirty cage that obviously hasn't been cleaned in weeks, and that's kind of a lightning rod topic.
More to the point of helping your snake since you care enough to go to the trouble to ask:
Your snake might have refused to drink the bad water and might be little dehydrated, that would clear up quickly with fresh water. Could something else have happened while you were gone, did the tank get exposed to direct sunshine, or cold draft, or another pet harass the snake? Did you have a "snake-sitter" look after it?
Barring those sorts of issues having to do with your time away, has your snake gotten gradually thinner, or just suddenly changed?
If gradually then either diet or temps/environment is suspect, either frequency of feeding(many folks feed corns every week, as opposed to boids which go longer...) or else nutrition... If you are feeding full grown mice for example, there should be enough calcium for the snake's health, but baby mice might not have enough, dusting the prey with calcium "herp-dust" might help, some folks put drops in the water dish that have calcium in them...all these products claim to have additional vitamin benefits, too.
If the snake has gone off feed, it might be a spring thing, but if it is eating well, has no other sudden stresses, but declines suddenly, disease or old age should be considered.
Hopefully I've given you some ideas to think about and I hope you will follow up with us, we'd like to help!
One great all around source of info (blatant plug warning!) is Kathy and Bill Love's definitive book, ?"Corn Care Manual"? I think the cover is worn off mine so I forget exactly what the title is! Check for that in your local pet shop or on their website Cornutopia, which has a lot of care sheets there too...
Good luck to you and your snake-