If the main site means for you the "master" website, the solution that I see is in the .htaccess where you should write an additional rule to redirect the website URL.
I think that you should write something like:
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteCond %{HTTP_HOST} ^
www.mysite.com/mysubsite1$
RewriteRule (.*)
www.mysite.com/mysubsite1/$1 [R=301,L]
</IfModule>
I didn't tested. This is just to help you get inspired of something.
Becarefull that when you do that, you will loose the access to your master.
To access your master, you will have to use another domain (or subdomain) that is not defined in any slave site.
Now if the "main" site is also a slave site then in JMS, you can update the site definition in which you add the "main" site URL into the "subsite1" definition.
In "subsite1" definition, you can also select "redirect to the first domain".
So if in the "subsite1" definition you have:
www.mysite.com/mysubsite1
www.mysite.com
Select to the first one, will redirect
www.mysite.com to the "first"
www.mysite.com/mysubsite1