Compound TCP by Microsoft is just one implementation of a congestion algorithm protocol. In Linux this has been discarded as you've already found, and it seems that TCP Illinois was the direct successor, but not used that much any more.
Some work has been done to implement Illinois since 2.6.22: LWN article: TCP Illinois preliminary version. It also seems still available in current versions:
net/ipv4/tcp_illinois.c in linux-stable tree.
TCP New Reno, another alternative based on RFC3782 seems to be the most commonly used in Linux and completely integrated in the kernel. See also the manpage
tcp_available_congestion_control (String; read-only; since Linux 2.4.20)
Show a list of the congestion-control algorithms that are registered. This
list is a limiting set for the list in tcp_allowed_congestion_control. More
congestion-control algorithms may be available as modules, but not loaded.
Check the ones available on your system:
Change the active one by writing to it (example
echo reno | sudo tee /proc/sys/net/ipv4/tcp_congestion_control
Bottom line: You're probably already using a very modern and very efficient TCP congestion algorithm protocol just by using a recent Linux kernel.