Might as well check for the illegal state and throw an exception

public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java

@@ -1010,6 +1010,8 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
             for ( byte b : indelStr )
                 sb.append((char)b);
             cigar.add(new CigarElement(indelStr.length, CigarOperator.I));
+        } else {
+            throw new ReviewedStingException("Creating an alternate consensus from a complex indel is not allowed");
         }
 
         if ( reference.length - refIdx > 0 )