SCR crowbar circuit gate voltage?
My concern is that the leakage current through D1 will place the gate
voltage at at least 1.1V due to the forward drop of the 1N4007

The leakage current of a 1N4759 zener diode is about 5 μA: -

So, this current will be insignificant for voltages of 48 volts and probably will be until the voltage is in the low 50s and this will probably be sufficient for crowbar protection.

that leakage current will amplify and cause power loss through the SCR

Miniscule power losses I would anticipate. It certainly won't cause the SCR to trigger until it rises to several mA typically so, check the SCR data sheet and find out what the typical trigger current is for that device.