Sorry this is probably way too late for you, but I'm experimenting with a WP MultiSite installation with BuddyPress and FeedWordPress. i only have four blogs, and there were a couple of minor issues so far - but it appears to be working quite well. My experience was similar to yours, so figured i'd share =)
i did not network activate the FWP plugin, but i installed it as Site SuperAdmin and then went into a subdomain blog to activate the plugin and start testing the feeds. i have over 30 feeds installed, although some 8-10 more were "rejected" by FWP.
The issues i spoke of were the initial activation of the plugin caused a site-wide redirect bug - i had to FTP in, backup the newly created feedwordpress folder, and then delete the feedwordpress folder from the wp-content/plugins folder before i could log onto the site.
Gave me a bit of a shock, but once i logged in there was no problem re-uploading the feedwordpress subfolder to the plugins folder, no need to hassle with deactivating or uninstalling the plugin. It just "worked" after that initial hiccup.
FeedWordPress author Charles Johnson has also written some nice plugins (call them FWP+) which offer a lot of enhancement to the core FWP plugin - and are also free. They should probably be installed prior to the initial synchronization with the feeds, to maximize continuity of appearance and other logistics.