Gmail has a notion of "me" as a sender and recipient, which is why searching your mail "from:me" works.
If you choose "Treat as alias," Gmail will treat the other address as "me" in addition to your main Gmail address. If you untick "Treat as alias," then it won't. Before this feature was added, all "send mail as" addresses were treated as aliases, or in other words, treated as "me."
There are a few minor repercussions. For example, if you send a message to "me," Gmail will put the message into your inbox. So if you send a message to address B, then Gmail will put it in the inbox if B is treated as an alias, but will not put it in the inbox if B is not treated as an alias.
"Treat as alias" does not affect whether your other address shows in the headers; that feature is controlled by your choice to use an SMTP server for the other address. It will also not affect specific searches for the other address, or your default reply address (e.g. "Reply from the same address the message was sent to").
You should use "Treat as alias" if the other address represents your own personal identity. You should not use "Treat as alias" if the other address represents another person (such as your boss) or a mailing list.
When you choose to use the SMTP server for the other adress and do not check the 'Treat as alias' box, a bug in gmail occurs. All mail sent by you as account B will appear as sent 'to:me' in your Sent Mail box. See this thread. While this bug remains unfixed, it is highly recommended to use "Treat as alias".
Finally, I have found source of the problem and want to share it for others, having the same problem.
It turned out, that I accidentally unchecked Treat as an alias checkbox for my main account, on Settings → Accounts and Import → [account name] → edit info. After checking it back (this time for all my accounts) entire Reply functionality got back to normal.
Turns out, that this is not a bug, but some kind of feature, about which Google is aware and have it described in details. Most important parts:
If you use Gmail's Send mail as feature to send messages on behalf of another email account, you may encounter the following issues: (...) If you receive a message from a Send mail as address and you click Reply, the To: field is incorrectly populated with your primary address. (...) These issues occur because Gmail treats your Send mail as address as an alias of your primary address. You can change this behavior in your mail settings by deselecting Treat as an alias.
And now, comes the best part. Either I'm missing something, or in my case the solution was to do something exactly opposite to what Google suggests! From my understanding of above text (correct me, if I'm wrong), I should deselect Treat as an alias to fix the problem, that To: field is being incorrectly populated with my primary address (that is exactly, what was happening to me).
Well, the problem is, that I was experiencing above mentioned problems when I had Treat as an alias checkbox unselected. And selecting it back solved the problem. Only after then my To: field started to become correctly populated—exactly how it is described in Kevan Sheridan's answer.
Best Answer
In short, no you can't. You can use the 'automatic vacation' responder found on the first page of settings within GMail to set a specific date, however you're going to have to do that at the end of each week.
More here - http://support.google.com/mail/bin/answer.py?hl=en&answer=25922