Hi Sridhar,
As per SAP help, update command within ABAP code is 100% supported. The situation which you have is a result of poor ABAP program where update command is not used in a desired manner.
SAP recommends to update a custom table from internal table using update or insert command.
Direct updates to custom or std table is not recommended by SAP.
Hope this helps.
Regards,
Deepak Kori