If the salary is paid by your branch or associate company abroad to the employee for the services rendered outside India, such salary income is not taxable in India, as the income is not accruing in India to such employee.
If the salary is paid by the company from India for the services rendered outside India, though the income is not accruing or arising in India, still there may be ground for the assessment of such income in India, if the employee's services are indirectly connected with Indian operations. Hence, it is not advisable to pay salary from India, which is also your plan as mentioned in your query.
The employee, though a non-resident will still be assessable in India if he has income like rent and interest. He will have to pay taxes in India by way of TDS and file returns on such income in India. However, he will be able to claim double taxation relief in the country in which his salary income is assessed, if there is double taxation relief treaty between India and such country.
To minimize his tax burden in the host foreign country, he needs to be careful about his residential status by not staying in India for 182 or more days in a financial year. Otherwise, his foreign income will also be added to his income in India, if he is treated as a Resident in India. This will unnecessarily complicate his returns in India as well as the host foreign country.