You can't remove the frigate factory from the playerrace file, but you can make it so that you can't build it. The best way would be to give the frigate an research prerequisite which you can't get such as a researchsubject from one of the other races.
btw exactly what did you mean with the frigate factory line. All you could do is just this for every playerrace.entity:
entities
planetModuleInfo
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count 9 - change to 8
entityDefName "PLANETMODULE_TECHORBITALMETALEXTRACTOR"
entityDefName "PLANETMODULE_TECHORBITALFRIGATEFACTORY" - remove this line.
entityDefName "PLANETMODULE_TECHORBITALCOMBATLABORATORY"
entityDefName "PLANETMODULE_TECHORBITALTRADEPORT"
entityDefName "PLANETMODULE_TECHORBITALCULTURECENTER"
entityDefName "PLANETMODULE_TECHORBITALCRYSTALEXTRACTOR"
entityDefName "PLANETMODULE_TECHORBITALCAPITALSHIPFACTORY"
entityDefName "PLANETMODULE_TECHORBITALNONCOMBATLABORATORY"
entityDefName "PLANETMODULE_TECHORBITALREFINERY"
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count 7
entityDefName "PLANETMODULE_TECHORBITALGAUSSDEFENSE"
entityDefName "PLANETMODULE_TECHORBITALHANGARDEFENSE"
entityDefName "PLANETMODULE_TECHORBITALREPAIRPLATFORM"
entityDefName "PLANETMODULE_TECHORBITALJUMPBLOCKER"
entityDefName "PLANETMODULE_TECHORBITALSHIELDGENERATOR"
entityDefName "PLANETMODULE_TECHORBITALCANNON"
entityDefName "PLANETMODULE_TECHDEEPSPACEMINE"