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Baseline average time (in 1.517-SNAPSHOT) of Util.getDigestOf(new FileInputStream("…/jenkins-war-1.509.1.war")): 220msec.
Using a BufferedInputStream with default buffer size: 193msec.
Using direct buffer update rather than DigestInputStream saves nothing, nor does using MappedByteBuffer on FileChannel, nor does using DigestUtils, nor does using a larger temporary buffer.
Fast MD5 Implementation in Java takes 183msec, which is barely faster, but it requires JNI and is LGPL.
So I think I will switch to DigestUtils just to reduce custom code, and add buffering.