Can an employer charge employee/contractor a processing fee for payment?
No. The matter depends on whether the person qualifies as employee for purposes of the British Columbia Employment Standards Act. Your description suggests that you meet criterion (b) of the definition of employee insofar as you are (i.e., if you are) "a person an employer allows, directly or indirectly, to perform work normally performed by an employee". See section 1(1) of the Act.
Section 21(1) prohibits an employer to "directly or indirectly, withhold, deduct or require payment of all or part of an employee's wages for any purpose", and item (2) prohibits the employer to "require an employee to pay any of the employer's business costs except as permitted by the regulations". There is no indication that the alleged business cost of e-transfers would be one such exception.
do I have any recourse for such a small amount of money that isn't worth starting a law suit over?
You have the option to file a complaint in "an office of the Employment Standards Branch". See sections 74 et seq for further details.
You are not specifying the amount of the e-transfer that is being deducted from your compensation. The smaller the amount(s) at issue, the more important it will be for your complaint to persuasively explain how it is not "frivolous, vexatious or trivial". See section 76(c).
Directing the employer's attention to the aforementioned statutory prohibition prior to filing a complaint tends to disprove allegations of vexation. That is because you are giving the employer an opportunity to mend its conduct and avert the proceedings that otherwise would take place. That being said, a very occasional cost of few cents is very likely to lead to a conclusion of vexation or bad faith regardless of your preliminary steps.
In most other contexts, though, it is in your best interest to stay aware of the obligations that are being presented/proposed to you so that your actions do not constitute an acceptance of terms & conditions you would rather reject. Not all contracts come in the form of a written document signed by the parties.