IMO, this was one of the major drawbacks to MobileMe. If you set up a MM account in iOS, the sending address (i.e. From) was set to the MM address and couldn't be changed. Worse, if you used their SMTP server(s) to send your emails (from other mail clients that allowed you to set a different From address), the message would actually be edited so that the From address was the MM address. IOW, you could NOT use any other sending (From) address, which as pointed out above, if you already have your own domain and address is just not acceptable. In fact, IMO I think there ought to be a law against this type of tampering with a user/customer's private information in their messages. I know every server an email message passes through adds on its own Recieved header, but to meddle with the information that was put there specifically by the sender is totally out of order.😠 But Apple are not the only ones to indulge in this heinous practice.
Sadly, iCloud is no different in this respect. 😟
So, the answer is, don't set up your email accounts on your iOS device as type MobileMe or iCLoud. Set them up as basic IMAP accounts. This will allow you to use your actual MM or iCloud account(s) for email, but you can use whatever sending (From) address you like and pick a different SMTP server that will not meddle with your email data. This latter can be tricky, but I (like many others) can use my ISP for that. Otherwise you could try Google or Yahoo, but they can impose restrictions so be careful who you choose.
So, for each actual iCLoud account you have, set up an iCloud account on your device, take note of the incoming email server it automatically picks (probably p??-imap.mail.me.com), then turn mail OFF for that account. I also turn off Notes since that's tied into email so it makes sense. Then create another account, but choose Other, then IMAP and use the incoming server address you noted from the iCLoud account. At the end of the setup, ensure Mail and Notes are ON and you should be good to go.
What this means is you still use iCLoud for eveything that it provides (and that you want), but you use a local IMAP account for Mail and Notes and the local iCloud account for everything else. Using this approach allows you to use whatever addressing you want to send from and your iCloud (or MM) address is simply not listed so you cannot pick it by mistake. Plus you can use any SMTP server you want, so DON'T use Apple's and your chosen From address will remain intact in all your emails.
Regarding configuring the SMTP server(s), this is still an utter mess on iOS, even iOS 5. If you configure a second account with the same server as the first one, you get 2 identical servers in the list and you cannot really get around this. With a lot of messing about you can sometimes get to delete a server, but you need to exploit another bug in this part of the system to do so. It really is a crock of **** and Apple should be ashamed of themselves. On the Mac it's perfect. You can edit the list, adding, editing and deleting servers at will and picking which you want for each account, but on iOS it's an appalling **** up. However, after much messing about, I have been able to get 4 accounts all using the correct 3 servers in the required order, but it shouldn't and doesn't need to be this hard.
Apart from that last issue, the above setup is the best way I've found for using Apple's MobileMe and now iCLoud service, while avoiding the onerous restrictions placed on the use of their service by which you would otherwise be hamstrung. Some of you will quickly see that this method means 2 accounts on your device for each actual iCloud account, but this is not a major deal once they're set up. I use 4 iCLoud accounts and so I have to have 8 actual accounts, but the only place I see this in iOS is in 'Settings/Mail, Contacts and Calendars' where I set them all up. In Mail I can only see 4, because there's only 4 email accounts. Likewise in Contacts, I can only see 4 accounts, because there's only 4 accounts that are set to handle Contacts. In fact, if I only wanted 1 Contacts and 1 iCal account I could just have a total of 6 accounts. So you have complete flexibility over the setup. The only thing to ensure is you only use IMAP accounts to handle email.
Hope this helps some people.