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1. I think so. When restoring a site the second to final page is the Replace Data page. You have two boxes, from and to. You can add one line in the from box reading http://www.example.com and a corresponding line in the second box reading https://www.example.com (where www.example.com is of course to be substituted with your site's domain name). Also take care to change any URLs in the right-hand side box starting with http:// to https://

That said, you're better off not going through that trouble with just two .htaccess changes:

# Redirect all HTTP requests to HTTPS
RewriteEngine On
RewriteCond %{HTTPS} !=on
RewriteRule ^ https://%{HTTP_HOST}%{REQUEST_URI} [L,R=301]

# Enable the HSTS header which tells the browser to never try using plain HTTP on your site, EVEN THOUGH the URL uses http:// instead of https://
Header set Strict-Transport-Security "max-age=31536000" env=HTTPS

That's it. Your server and browser will work together and make sure that no user data travels through HTTP even though your URLs may be using http:// instead of https://.

2. No, this isn't possible. The main reason is how WordPress stores the data for the sites. You CAN exclude their database tables (the most practical way being with the RegEx Database Tables Exclusion feature), but the restored WordPress site will still list these sites. Removing individual sites requires a lot of database surgery and it's unlikely that instructions for WP 4.2 will work with a future version, e.g. WP 4.5 so we can't really add such a feature :(