Yes, fighters can come to all All Stop/break by hitting the <Delete> key. (Afterburners is <Insert>).
Removing the homing torpedoes on a fighter is pretty easily done, as is tweaking the beams to the level of inadequecy you see fit. The main problem is that each species can only have one fighter which means that this shuttle will become the default Terran player fighter instead of the Allard FXI.
Depending on what capabilities you wanted to assign to it and how much GM overhead you wanted to allocate to this idea, you could simply mock up a shuttle as a capital ship and have officers transfer their consoles to the fighter when crewing it. This has the benefit of leaving other fighters unaffected, allowing multiple officers to participate on a shuttle mission or leaving shuttle combat somewhat clunky for a single pilot/gunner, as well as enable them to assist their mothership with alternate taunting vectors and an auxiliary science relay depending on how many stations are selected. This way would also mean the shuttle could be slightly more capable if desired since it couldn’t be launched and disposed of at will. It just requires GM attention to appropriately set up the launch and then recovery/silent destruction on return.