Groovy's XML capabilities are powerful enough that you may not need to consider other alternatives such as XQuery. If you wish to use XQuery though, it isn't hard to do. Here we just added mxquery.jar from the MXQuery project to our CLASSPATH.
Once our path is set up, we can run the following script:

// require(url:'http://www.mxquery.org', jar:'mxquery.jar', version:'0.4.1')
import ch.ethz.mxquery.query.Context
import ch.ethz.mxquery.query.impl.CompilerImpl
import static ch.ethz.mxquery.util.IteratorPrinter.*

def query1 = 'for $seq in (1,2,3,4,5) where $seq mod 2 eq 0 return $seq'
def context = new Context()
def compiler = new CompilerImpl()
def result = compiler.compile(context, query1).evaluate()
println eventsToString(result)
// =>
// 0: [12815	xs:integer 2]
// 1: [12815	xs:integer 4]
// 2: [64	END_SEQUENCE]

def query2 = '''
    copy $x := <doc><el><node>this node is deleted</node></el></doc>
    modify
    (
        delete node $x/el/node,
        insert node <node>this node is inserted</node> into $x/el
    )
    return $x/el
'''
result = compiler.compile(context, query2).evaluate()
println XMLPrettyPrint(eventsToXML(result).toString())
// =>
// <el>
//   <node>
//     this node is inserted
//   </node>
// </el>

Depending on your XQuery processor and operating system, you might be able to make use of XQuery directly from the command line instead of calling it from Java or Groovy.