There are various important questions that have to do with occasions of conflicting responsibilities to our fellow man and to our Maker. There is no sweeping answer that addresses all of the questions, but there is source material on a variety of cases that can give us guidance.
Tefilla b’tzibbur (davening with a minyan) is very important.[1] Although there are indications that it is just a way to fulfill the mitzva of tefilla more fully (b’hidur), Rav Moshe Feinstein understood tefilla b’tzibbur as an independent obligation.[2] In any case, the poskim mention some of the parameters concerning to what extent one must go in order to daven with a minyan.
One must travel up to eighteen minutes in order to attend a minyan.[3] If going to a minyan will cost a person money (apparently, beyond small expenses such as paying for a few ounces of gas), he is not required to go. However, if one merely thinks that he can gain money by missing minyan, he should attend minyan.[4] If one has a set job from which wages will be deducted for time spent on davening at a minyan, this is considered a monetary loss, and one is not required to go. However, a ben Torah who finds that he is in a good financial situation should consider agreeing to a small reduction in pay in order to be able to daven with a minyan. Whenever a person judges whether to accept a job, in addition to considering the salary, he takes “quality of life” factors into account, as well. Among the personal and religious factors that are unique to shomrei mitzvot and b’nei Torah should be the matter of tefilla b’tzibbur.
When one has responsibilities at work, he is required by halacha to take them very seriously. Berachot 16a poignantly illustrates how Chazal were prepared to lower certain religious obligations (like the optimal manner of davening and bentching) to avoid infringing upon the careful fulfillment of one’s responsibilities to his employer. Thus, sneaking out is not a halachic option. That same gemara mentions that if the employer is not bothered by the employee’s normal fulfillment of tefillot and berachot, then he should daven and bentch normally.
Therefore, you should raise this matter politely with your boss (without risking your job) and see whether something can be worked out (e.g., you can offer to come in early). You can also investigate whether you can find an early or a late minyan (certainly, if it is within an eighteen-minute radius) in order to obviate the problem.