If you are using Java agent pre-10.7, it is not possible to skip SOAP errors.
If you are using 10.7, the java agent code has been enhanced to include this idea :
SPM SOAP Faults should follow Standard Error Processing - https://communities.ca.com/ideas/235731711
This enhancement is available as 10.7 HOTFIX# 13
To obtain a copy of this HOTFIX contact CA Support.