You asked several questions in one.
- I suppose that I might get rejected, but will this have negative impact for me?
- Should I contact the editor already now?
- ... should I interrupt the process, or wait and see what happens?
Starting with #3. You should keep calm and enjoy the process unfolds.
- A targeted journal need not perfectly match. Though there should be some matching. Hence why journals post their 'aim', 'scope', and 'about'.
- Another indicator of #match is alignment between your reference list, authors and journals.
Invariably #3 answers #2. You don't have to contact the editor already.
Before addressing #1, seemly you have a #4.
- The 'fear' should be having ('low-impact) article(s) in shaky or low-impact journals. That is what would 'shed a bad light on' a possible future academic career.
- Having a shot at discipline's foremost high-ranking journal is a target every researcher should attempt. With the right mindset (well-conditioned 'thick skin'), there's much to be gained from the review process. Yes, some reviewers can be obnoxious and condescending. Looking beyond the (review) text and looking within the review text (reading in-between the line) is key to improving one's manuscript (and making adjustment to the research work where need be.
As to your #1, a rejection does not impact negatively.
In between, rejection is a fabric we all wear with pride as researchers. Fearing rejection as academia is fearing to excel.
Contribution to knowledge comes in many ways. Novelty is not only in 'new frontiers'. Novelty can come from 'improvement and extension of already existing methods'. The shift in the existing method might (go ahead to) make a groundbreaking impact on the discipline. Discussing 'novel/novelty' might take us to discuss #philosophy, which might distract us from your question. [For a few pointers to the philosophy of novel/novelty, see James, 1979; Miller, 1950; Cohen, 2017]. This quote from Cohen, 2017 might lead to other nuances of novelty. I would venture into those here.
“(T)he primary novelty of this work is the ability to make a prediction about drug sensitivity. Reviewers felt that the predictive ability would be very hard to generalize, however, reducing the impact of this novel feature. This concern about novelty… was the driving factor in this decision.” -excerpt from a rejection letter received by the author
Novel/novelty might also lead us into the terrain of positivism, interpretivism, pragmatism, critical realism and the rest of research philosophy. It appears novel/novelty might have been part of the driver of Roy Bhaskar in his ferocious 'development' of critical realism.
Be it as it may, since your 'article is in its second revision stage', go through the process, develop strong rebuttal skills and insightful communication. You'll need them in your 'future career'. The world is your oyster.
Parting shot: Your research work has already caught the attention of the Editor. You've scaled through desk reject. Don't abort!!!
James, W. (1979). Some problems of philosophy (Vol. 7). Harvard University Press
Miller, D. L. (1950). Novelty and Continuity. The Journal of Philosophy, 47(13), 369-378
Cohen, B. A. (2017). How should novelty be valued in science?. Elife, 6, e28699