Am I right to be concerned and to want to avoid using the ObjectUtils.equals() where ever possible?

No. What you need to consider equals depends on your requirements. And wanting to consider two nulls equal and any non-null unequal to a null without having to deal with NullPointerExceptions is a very, very common requirement (e.g. when you want to fire value-change events from a setter).

Actually, it's how equals() in general should work, and typically, half of that behvaiour is implemented (the API doc of Object.equals() states "For any non-null reference value x, x.equals(null) should return false.") - that it doesn't work the other way round is mainly due to technical restrictions (the language was designed without multiple dispatch to be simpler).

Using Java 8:

private static Comparator<String> nullSafeStringComparator = Comparator
        .nullsFirst(String::compareToIgnoreCase); 

private static Comparator<Metadata> metadataComparator = Comparator
        .comparing(Metadata::getName, nullSafeStringComparator)
        .thenComparing(Metadata::getValue, nullSafeStringComparator);

public int compareTo(Metadata that) {
    return metadataComparator.compare(this, that);
}