The more loyalty points you accumilate the better the offers you will recieve. Generally speaking they arent really worth saving until your on level 3 agents, until then just cash them in for items you would find useful.
I would reccomend a webber on that merlin, and 150mm rail guns, they hit better and the tracking defacit is negated by the webber.
If you keep whoring that agent and train connections to lvl 2/3 you will be able to jump into lvl 2/3 agents immediately, you will recieve a standing increase for each mission you complete, allowing you access to better agents within that faction. Other than that loyalty/standing only effects your reprocessing rates at stations.