You can specify *some* variables on the command line, eg
./runInstaller -ignoreSysPrereqs -ignorePrereq -waitforcompletion -showProgress -silent ORACLE_HOME=%ORACLE_HOME% etc
but I'm not sure if TNS_ADMIN is one of them. If not, I think the only way to achieve this would be to unset TNS_ADMIN before running the silent install. So if you were doing this in a batch file you could do something like
set PREV_TNS=%TNS_ADMIN%
set TNS_ADMIN=
[run silent install]
set TNS_ADMIN=%PREV_TNS%
or similar