I've done the Master-Cleanse several times, over the last few years. I've even become a something of a coach for others trying it. The last cleanse I did using bottled Organic Lemon juice.
It is definitely easier and cheaper using the bottled Organic Juice from Santa Cruz. To buy an organic lemon from our grocers is at least a dollar a piece. If it was cheaper there was a reason - the lemons weren't good.
I think doing the cleanse period is better than not doing it and the Organic Lemon juice definitely makes it more convenient. I also use the cleanse mixture as a daily snack when I'm not on the cleanse and having the bottled stuff is nice and easy.
I wouldn't over think it. The Lemon juice may be compromised slightly in the bottle - but will still be plenty beneficial to your cleanse. Even conventional lemons will help if thats all there is.
The Cleanse is difficult enough - don't stress yourself out thinking about if your doing it right or wrong. Instead, use that energy to do it. You'll be fine!