[agent] Deprecated flags are ignored totally

[gouthamve]

When a deprecated flag, for example, --discovery.min-peers=50 is set and the corresponding replacement flag is not set, then we would need MinPeers to take the value of 50. But the actual value is set to 3.

https://github.com/jaegertracing/jaeger/blob/master/cmd/agent/app/reporter/tchannel/flags.go#L82-L83
would always overwrite this (i.e, with default values even if the new flags are not set):
https://github.com/jaegertracing/jaeger/blob/master/cmd/agent/app/reporter/tchannel/flags.go#L70-L77

I've noticed this while fixing the failing tests for my PR: #1034
The fix is in the last commit of that PR, but I can cherry pick that into another PR if you want.

[gouthamve]

Closed in #1034