Excess paid service tax can easily be adjusted against service tax liabiliy in the succeeding period provided the details thereof intimated to ST authorities at the time of filing relevant ST 3 return.
If not, you can show the excess paid CENVAT details in your monthly excise return and adjust subsequently.
Refund of service tax could be the last option in practice, since filing Form R and necessary representation to ST authorities is time taking process (2 to 4 months time genereally)