I tested the Activity Stream gadget on a Confluence page and all the issue links went straight to JIRA. I tested with JIRA 7.3.6 and Confluence 6.3.1.
I found a bug report for the behavior which has not been reported fixed: Links from JIRA Use Relative URLs for Activity Stream. Yet I could not reproduce it. A customer posted a workaround on the bug report.
Please let me know in what versions of Confluence and JIRA you are seeing the bad links when you use the gadget.
I had a 6.3.x JIRA test instance and when I tested with that linked to my Confluence 6 instance I got the relative URLs as you report. Somehow Links from JIRA Use Relative URLs for Activity was resolved in a later version of JIRA.
I hope you can upgrade soon because 6.x has passed End of Life status.
I will comment on the bug to let people know it is not impacting JIRA 7.3.6.
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