Will I be rewarded for praying Fajr in congregation if I pray it at home due to security conditions, knowing that I am keen to pray Isha in the mosque?

There is no blame upon you for missing Fajr prayer if you fear for yourself, for "fear for oneself" is an excuse that permits abstaining from congregational prayer. We hope that Allah will record for you the reward of congregational prayer, for the Sunnah (definition) indicates that a servant is rewarded for the good deeds they habitually performed if they become unable to do them. If it is possible for you to establish the congregation in your home, then do so, for congregational prayer is obligatory even if not in the mosque.