Before I answer, I have to say that I disagree with several claims stated/implied in your question:
antibiotics or any treatment cannot be simply replaced by another; many factors have to be taken into account, such as the type and severity of acne, the microorganism(s) (bacteria) causing the problem and many others
topical use of antibiotics definitely doesn't cause antibiotic resistance per se, but "The inappropriate use of antimicrobial drugs, including in animal husbandry, favours the emergence and selection of resistant strains, and poor infection prevention and control practices contribute to further emergence and spread of antimicrobial resistance." (WHO)
As for the side effects and potential risks of certain therapeutic options - no one can absolutely guarantee that every possible outcome is predicted, but if there is evidence that potential risks outweigh the benefits, the substance/product will not be approved by regulatory agencies.
That being said, there are natural (herbal based) therapeutic options for acne. One of them is:
Tea tree oil
Melaleuca alternifolia (Maiden and Betch) Cheel, Myrtaceae aetheroleum
According to EMeA's herbal monograph one of its therapeutic indications is:
Traditional herbal medicinal product for treatment of small boils (furuncles and mild acne)
The form in which it is used:
Herbal preparation in liquid and semi-solid dosage forms for cutaneous use
The same document contains precautions, side effects, contraindications, posology etc.
Antimicrobial activity of tea tree oil (TTO) has been confirmed:
- in vitro in various studies
Since you are interested in antibiotic resistance, this part might be the most interesting for you:
The activity of TTO against antibiotic-resistant bacteria has attracted considerable interest, with methicillin-resistant Staphylococcus aureus (MRSA) receiving the most attention thus far. Since the potential to use TTO against MRSA was first hypothesized (153), several groups have evaluated the activity of TTO against MRSA, beginning with Carson et al. (31), who examined 64 MRSA isolates from Australia and the United Kingdom, including 33 mupirocin-resistant isolates. The MICs and minimal bactericidal concentrations (MBCs) for the Australian isolates were 0.25% and 0.5%, respectively, while those for the United Kingdom isolates were 0.312% and 0.625%, respectively. Subsequent reports on the susceptibility of MRSA to TTO have similarly not shown great differences compared to antibiotic-sensitive organisms (39, 58, 68, 106, 115).
from: Melaleuca alternifolia (Tea Tree) Oil: a Review of Antimicrobial and Other Medicinal Properties C. F. Carson,1 K. A. Hammer,1 and T. V. Riley1,2,*, Clin Microbiol Rev. 2006 Jan; 19(1): 50–62.
- in vivo - clinical efficcacy in at least one study
By the same source:
One of the first rigorous clinical studies assessed the efficacy of 5% TTO in the treatment of acne by comparing it to 5% benzoyl peroxide (BP) (14). The study found that both treatments reduced the numbers of inflamed lesions, although BP performed significantly better than TTO. The BP group showed significantly less oiliness than the TTO group, whereas the TTO group showed significantly less scaling, pruritis, and dryness. Significantly fewer overall side effects were reported by the TTO group (27 of 61 patients) than by the BP group (50 of 63 patients).
Whether the effect will be bactericidal (killing bacteria) or bacteriostatic (stopping their reproduction) depends on the concentration:
TTO is for the most part bactericidal in nature, although it may be bacteriostatic at lower concentrations.