I was able to manage the CPU and memory consumptions of the Splunk agent using Intigua.
I was facing with this issue on my Exchenge servers and using Intigua I was able to throlle the CPU and memory consumption.
You can download it here: http://www.intigua.com/get-intigua
Have you tried disabling the recurse option on any monitor stanzas in inputs.conf?
I've had some issues with the 6.3.x forwarders and high cpu on using both the recurse option and wildcards in the monitor path. From my support requests it sounds like it's a known issue with short file names and there's a fix on the way.