For example we are peering with eth1 at 1GBits on one IXP and have 3 BGP upstream peers configured on this (receiving full BGP tables), no other BGP peers exist.
Do you guys have any idea or probably setup on rate limiting traffic for one or multiple of these upstream BGP peers?
E.g.
Peer 1: 100Mbps
Peer 2: 200Mbps
Peer 3: Full 1GBits
Depending on which version you are, VyOS 1.4 supports set protocols bgp parameters bestpath bandwidth and set policy route-map foo rule 10 set extcommunity bandwidth - that might do the trick.
For deeper information refer to BGP — FRR latest documentation
or use a shaper on the interfaces.