The simple answer is yes, but in application, probably no.
I'm going to go back to basics to try and explain what's going on. I'd say that this is from memory and might not be 100% technically accurate, but should be enough to make sense. No doubt the community will correct me (and fill in an gaps) :)
If we go back to the 90's (and I suppose earlier) when email and "the internet" was taking off, email systems are comparable to the postal system at a university with pidgin holes. POP3 is the Post Office Protocol (version 3).
- The Sender write a letter and wrap it in an envelope ready for sending.
- The Sender then takes the letter to a postbox.
- The letter gets routed to the recipients university's mail room.
- The mail-room staff put the letter into the correct pidgin hole for the recipient.
- The Recipient goes to the mail room to check their pidgin hole for mail.
- The Recipient takes any mail back up to his dorm room to read through it.
so looking at our computers now
- The Sender writes an email in your mail client and specify an address and other attributes within the header (envelope).
- The Sender connects to your SMTP server and send give sent it the mail.
- The Sender's SMTP server will work out the recipients mail server and deliver the email to them.
- The Recipient's mail server routes the email to the correct mailbox for the username.
- The Recipient checks for mail. Connecting to the POP3 server we check our inbox for mail.
- If we find any email, we download it for reading.
Ok, so POP3 lets is access our pidgin hole and grab everything in there. It was absolutely fine when people were keeping all their post at home on the one computer.
Shortly after, we find ourselves in a situation where people suddenly want to access the same data from multiple devices in multiple locations; person with multiple email clients on different devices (phone, work, home...) and also this whole cloud computing jango where we access everything via the web, or even worse, where we want all three.
This is where POP3 falls on its ass. Although as you've realised, you can set it not to delete the email once it downloads it, you're actually overriding the default functionality and this leads to interesting problems.
Its like getting the university mail room to take a photocopy of all of your letters. They will, but when you next come to collect your post they have no way of knowing whats new or what you already have a copy of. It can also be slow and bad tempered.
So, we get IMAP(4) coming along which helps to fix this problem.
Instead of your mail client grabbing everything from the remote server and dumping it into some specified local folder (inbox) IMAP is working with a remote set of folders and files and just keeping a local cache updated with whats going on on the server.
With all of your email staying on the server it means its always available to access on multiple devices or via webmail. The other bonus is that when you're downloading mail via IMAP rather than POP, its a lot more clever about synchronisation so you don't end up re-downloading the same emails all the time. You can set up different sync options for different folders which can make managing lots of emails easier.
So, in closing:
Any way to stop this without deleting them on the webmail side
On the webmail side, I would try and create a new folder and then move all of the emails from this mailing list into it. Hopefully outlook will only be downloading your 'inbox' folder and will therefore skip all those other emails.
If you can create email rules or filters in your webmail then you might be able to set it up to do this automatically.
and would this happen with IMAP protocol?
If you were using IMAP then when you deleted all those emails from outlook they would have been deleted on the server as well (as its just synchronised folders).
There is a good chance that your web host won't let you do server side filtering, so you would have to go and sort through manually in the webmail each time. Using IMAP means that you could create server side folders in outlook and use that to move mail into correct folders.
The other bonus, is that you could tell outlook to use the server side "sent" and "drafts" folders, so you could start drafting something in outlook and finish it in the webmail, or view mail sent through the webmail in outlook.
Hope this makes some sense :S