I'm assuming you want to use the ethernet interface for hacking value, but don't want to route your updates via the ethernet interface (which is what I am doing, too).

You need to edit /etc/tcphonehome.tcl.
It detects if there is an ethernet on your tivo and if there is it figures it can get the updates via this interface and doesn't even try to dial out.
I'm running version 1.5 of the tivo software so the following line numbers may be out for your tivo (but you'll get the gist):
in /etc/tcphonehome.tcl:
211: if { $fAddRoute } {
This whole block needs to go.
228: if { $Ether == 1 } {
You want to execute the else block instead.
371: if { $fAddRoute } {
This whole block needs to go.
383: if {$Ether == 0} {
remove the if statement, you DO want to execute this bit of code.

Obviously you could do something really clever and rewrite the whole code to differenciate between your ethernet interface and the one tivo might put in, but there is no real need.
You may want to save a backup copy of your tcphonehome.tcl of course...

Oh and you need to copy the original routing command back in. This obviously limits you to connecting to your tivo from the local subnet.

My /etc/rc.d/rc.sysinit ends like this (where route.none is the empty route command you created originally):
# Run the Phase 4 (background tasks have been started) scripts
runme phase4

tnlited 23 /bin/bash -login &
(insmod -f /lib/modules/8390.o && insmod -f /lib/modules/tivone.o)
(ifconfig eth0 192.168.140.59 netmask 255.255.255.0 up && route.none add default gw 192.168.140.22)

Hope this helps.
Eric