If you take out the '=' and use
pre-up ifconfig eth0 mtu 9000
then it takes it just fine.
debian:~# ifconfig
eth0 Link encap:Ethernet HWaddr 00:50:43:01:49:7a
inet addr:192.168.144.253 Bcast:192.168.144.255 Mask:255.255.255.0
inet6 addr: fe80::250:43ff:fe01:497a/64 Scope:Link
UP BROADCAST RUNNING MULTICAST MTU:9000 Metric:1
RX packets:64 errors:0 dropped:0 overruns:0 frame:0
TX packets:105 errors:0 dropped:0 overruns:0 carrier:0
collisions:0 txqueuelen:1000
RX bytes:10208 (9.9 KiB) TX bytes:81902 (79.9 KiB)
Interrupt:11
I can connect to it via the interface so it isn't completely broken even if it might not do what you want.
I should point out that mine was on a standard plug, no eSATA.