Cheap flights to Namibia are non-existent.
Your best bet will be with British Airways to Jo'burg for something like 600 GBP I guess.
Check the Windhoek Airport wiki page for more info on connections from Johannesburg or other possibilities.
There are some possibilities from Germany with flying with Condor or last-minute-charter.
See www.condor.com and www.lufthansa.com
This has the advantage that you do not have to leave from London for a cheap ticket, you can catch a budget flight to Germany and then leave from Germany, flying directly to Windhoek without a transfer in South Africa.