Update retrieval of t2.ID with 't2.ID as ID2' to assign it to ID2. Then you can use two unique output field names for ID columns.
<query id="q1" useConfig="s1">
<sql>Select t1.ID,t1.Table1Description,t2.ID as ID2,t2.Table2Description from Table1 t1 join Table2 t2 on t1.ID=t2.Table1_ID</sql>
<result element="Entries" rowName="Entry">
<element column="ID" name="ID1" xsdType="string"/>
<element column="Table1Description" name="Table1Description" xsdType="string"/>
<element column="ID2" name="ID2" xsdType="string"/>
<element column="Table2Description" name="Table2Description" xsdType="string"/>
</result>