According to the schema
element itself has a version
attribute:
<schema
attributeFormDefault = (qualified | unqualified) : unqualified
blockDefault = (#all | List of (extension | restriction | substitution)) : ''
elementFormDefault = (qualified | unqualified) : unqualified
finalDefault = (#all | List of (extension | restriction | list | union)) : ''
id = ID
targetNamespace = anyURI
version = token
xml:lang = language
{any attributes with non-schema namespace . . .}>
Content: ((include | import | redefine | annotation)*, (((simpleType | complexType | group | attributeGroup) | element | attribute | notation), annotation*)*)
</schema>
See http://www.w3.org/TR/xmlschema-1/#key-schema, "3.15.2 XML Representations of Schemas"
However, if you published the schema, then I think the best way to deal with it would be to use the target namespace. This would enforce the right version being used (but break compatibility)